Solved Windows 7 installation set external HDD as Active (and other problems)

[Kusuri]

So the first time I installed Windows 7 I left my 1TB eSATA external HDD (K: ) connected, even though it wasn't even being detected due to no drivers installed yet. AHCI was set in BIOS for both SATA and eSATA.

I installed W7 to a 90GB C:\ partition of an internal 640GB HDD . After the installation was done I removed the disk and used my PC as normal. After the next reboot it kept saying no disk in CD/DVD drive and wouldn't boot past that. I made sure in BIOS that the Boot priority was the HDD in which I installed the OS, but still no go.

What happened:
I did have the Windows folder in drive C:\, but I noticed that the external HDD was now Active and inside it had the following hidden system files: Boot folder, bootmgr, BOOTSECT.BAK.

I disconnected the external HDD and reinstalled Windows 7 to C:\. Didn't have problems this time.

However I am getting erratic behavior in my external HDD that I didn't have with Vista. I'm unsure if what happened during W7 installation is the reason for it, but normally 10 minutes after the ext HDD has been idle it goes to sleep (WD My Book). But since lately it has just started doing 2-3 second freezes in my PC after said time has passed, before shutting itself down. From then on onwards I'll keep having these freezes periodically and I can't soft-reboot or shutdown.

In Event Viewer several of these appear:

The driver for device  \Device\Scsi\JRAID detected a port timeout due to prolonged inactivity.  All associated busses were reset in an effort to clear the condition.

I decided to delete all the boot-related files from my ext HDD and used DISKPART to remove the "Active" flag. Didn't seem to help, however, so I'm wondering if it's a driver+Windows 7 incompatibility (which is strange considering I'm using the same driver that worked correctly in Vista).

I'm using specific JMicron drivers that made the HDD work as it should in Vista (waking up if I opened it after it was sleeping, instead of disconnecting itself), so why wouldn't it work in W7 as well? Or is this some other problem related to the first W7 installation? Might I add that it doesn't seem to happen all the time. Sometimes it does go to sleep and wakes up correctly in Windows 7, without doing freezes or giving JRAID events.

I've decided to boot into W7 Repair/Recovery console and run a chkdsk. Strangely enough it now says C: is X: and K: (ext. HDD) is now C:? Why is the external HDD being read as C: in the Recovery console? I have a 2nd internal HDD and it's kept its original drive letter (E: ).

How did the W7 installation even decide to set the external HDD as Active and create bootmgr files if I told it to install to a partition in the 640GB internal HDD??

Could it be a problem related to the MBR in external HDD or something?

Thanks

 

[Maguscreed]

You should never install the OS with an external drive attached. You're probably going to need to do this again, because windows put it's boot files on the external drive.
For future reference it's recommended that you not have any extra devices attached when installing. (keyboard and mouse only) I have even seen a number of guides that suggest pulling ram over 2 gigs.
You could repair the bootmgr for this but I'm guessing the log errors would continue even if you managed to repair the startup with startup repair.

 

[Kusuri]

Do what again exactly?

I did reinstall W7 with the external HDD unattached. Also removed the "Active" flag from it. That helped in being able to boot correctly, but have the strange JRAID timeout behavior sometimes when it's about to go to sleep.

Think I should reformat and install Vista instead, just to make sure the ext HDD problems aren't somehow being caused by W7 incompatibilities?

Was also thinking of reformatting the ext. HDD, but I'm afraid I don't have enough space in other drives to make a backup

 

[Maguscreed]

Well now that it has the boot records on it, it's probably giving it issue being detected properly, the problem will probably extend to vista.
Also see here.
Removing Win7 Bootmgr

 

[theog]

1) Copy & Paste the Boot files on the Ext Hdd to the OS drive.reboot.
2) remove Ext Hdd.
3) Boot up.
4) Do a startup repair.
http://www.sevenforums.com/tutorials/681-startup-repair.html?ltr=S
Note: You may need to do startup repair 3 to 4 times.
http://www.sevenforums.com/tutorials/105541-startup-repair-run-3-separate-times.html

 

[Kusuri]

But I no longer have bootmgr or related files in the ext HDD as I deleted them. Only the C:\ drive has them, as it should. Don't you mean I should fix the MBR of the ext HDD or something?

 

[theog]

But I no longer have bootmgr or related files in the ext HDD as I deleted them. Only the C:\ drive has them, as it should. Don't you mean I should fix the MBR of the ext HDD or something?

Just go to Step 2.

 

[whs]

You can try to fix the MBR on the external - e.g. with this program: Best Free Partition Manager Freeware for Windows 7, Windows Vista, and Windows XP 32 bit & 64 bit. MiniTool Free Partition Manager Software Home Edition.

 

[karlsnooks]

Kusuri,

Was you previous install where the drive worked on a 32 bit system?

32 bit drivers won't work on a 64 bit system.

If you have installed 64 bit drivers and the 64 bit drivers are for Win 7 then the drivers should be ok, but I suspect that the driver itself is the problem.

 

[Kusuri]

Both Vista I had and 7 are 64 bit.

Ok I'll try startup repair with ext HDD disconnected, but note I have no problems in the actual startup at the moment, just problems while using my PC with the ext HDD causing freezes when going to sleep and JRAID timout error events.

And will also try the MBR fix program, thanks.

 

[gregrocker]

You don't need Startup Repair if Win7 is booting correctly.

Short of moving the data off to wipe the external and reformat, you may need to manually remove the bootsecting in addition to the Active flag and boot files you've already removed.

I'm looking for the exact command now, to specify the external drive letter. Don't run the one in the TechRepublic thread as 52 is for XP while 60 is for Vista/7.

 

[theog]

You don't need Startup Repair if Win7 is booting correctly.

Short of moving the data off to wipe the external and reformat, you may need to manually remove the bootsecting in addition to the Active flag and boot files you've already removed.

I'm looking for the exact command now, to specify the external drive letter. Don't run the one in the TechRepublic thread as 52 is for XP while 60 is for Vista/7.

http://www.sevenforums.com/tutorials/20864-mbr-restore-windows-7-master-boot-record.html

 

[Kusuri]

You don't need Startup Repair if Win7 is booting correctly.

Short of moving the data off to wipe the external and reformat, you may need to manually remove the bootsecting in addition to the Active flag and boot files you've already removed.

I'm looking for the exact command now, to specify the external drive letter. Don't run the one in the TechRepublic thread as 52 is for XP while 60 is for Vista/7.

http://www.sevenforums.com/tutorials/20864-mbr-restore-windows-7-master-boot-record.html

You don't need Startup Repair if Win7 is booting correctly.

Short of moving the data off to wipe the external and reformat, you may need to manually remove the bootsecting in addition to the Active flag and boot files you've already removed.

I'm looking for the exact command now, to specify the external drive letter. Don't run the one in the TechRepublic thread as 52 is for XP while 60 is for Vista/7.

Thanks for everyone's replies.

I used the DISKPART command to remove the Active flag, but as far as removing the bootsecting I'm not sure. Only hidden files I could find and remove were BOOTSECT.BAK, bootmgr and Boot folder.

From the MBR-restore link you've sent me I see the bootsect.exe was supposed to be inside that Boot folder?

Even so could it still think the ext HDD is tied to the OS and booting somehow?

Why did W7 installation messed with the external HDD anyway? Is it because it read it as Drive C:\ during one of the reboots or something?

Oh, and the MBR-fixing won't make my ext HDD have boot files again right? Just to make sure.
I'll try it later when I get back home, thanks.

 

[theog]

1) EXT HD was plug in when Windows 7 or Vista was install at some time.

2) HD come from a PC with Windows 7 or Vista install on that drive & not reformat.

 

[Kusuri]

1) EXT HD was plug in when Windows 7 or Vista was install at some time.

2) HD come from a PC with Windows 7 or Vista install on that drive & not reformat.

Yeah it's 1), but why? It didn't mess with my other internal HDD. Why did it treat the ext HDD as related to OS install?

 

[Maguscreed]

This is something people have actually be complaining about. The installation will generally dump the boot files on whatever disk it sees as disk 0 at the time of install.
This is regardless of whether internal / eternal or even the drive you pointed to in order to install the OS.
I have actually taken to unplugging everything but the target drive when doing installs.

 

[gregrocker]

Even so could it still think the ext HDD is tied to the OS and booting somehow?

Yes, even though files are removed bootsect code is written to the HD bootsector, requiring running Diskpart Clean command to wipe.

Why did W7 installation messed with the external HDD anyway? Is it because it read it as Drive C:\ during one of the reboots or something?

It should not have messed with External HD as Windows does not install upon USB-connected Devices. Was it connected eSATA?

Oh, and the MBR-fixing won't make my ext HDD have boot files again right? Just to make sure.

There is no reason to repair the MBR on the Win7 HD if Win7 is booting correctly.

I've PM'd my teacher SIW2 for the exact bootsect command to remove bootsect code from your external. The best way remains to move the data off and wipe the external using Diskpart or free Partition Wizard bootable CD. Clean and Clean All with Diskpart Command

 

[Kusuri]

It should not have messed with External HD as Windows does not install upon USB-connected Devices. Was it connected eSATA?

Exactly, connected through eSATA... It was indeed the problem, I had no idea it would happen.

I've PM'd my teacher SIW2 for the exact bootsect command to remove bootsect code from your external. The best way remains to move the data off and wipe the external using Diskpart or free Partition Wizard bootable CD. Clean and Clean All with Diskpart Command

Thanks. I might actually consider doing a Clean All on all my 3 drives, even. Even if that takes 3 days... Just going to try and see if I can find some way to back up all the data that's in the external HDD...

Thanks.

 

[gregrocker]

If you plan to reinstall, follow these steps to get a perfect reinstall: Reinstalling Windows 7

However this shouldn't affect Win7 at all if it is now labeled System Active Boot in Disk Management as it is repaired and fully self-contained now.

What are the exact symptoms of the problems which are continuiing with your external?

 

[Kusuri]

If you plan to reinstall, follow these steps to get a perfect reinstall: Reinstalling Windows 7

However this shouldn't affect Win7 at all if it is now labeled System Active Boot in Disk Management as it is repaired and fully self-contained now.

What are the exact symptoms of the problems which are continuiing with your external?

It'll disconnect itself, even if I'm copying files, with several JRAID event error starting to appear periodically (every 1 minute or so) in the System Event Log:

The driver for device \Device\Scsi\JRAID detected a port timeout due to prolonged inactivity. All associated busses were reset in an effort to clear the condition.

When each of those errors happen I'll get a 3 second freeze in which I can't move my mouse. Also if I tell my PC to reboot or shutdown via start menu it'll just stay there saying "Shutting down...". Reconnecting the HDD doesn't help either. I have to hard-reboot.