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 Windows 7 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.
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 Windows 7 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 Windows 7 as well? Or is this some other problem related to the first Windows 7 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 Windows 7 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 Windows 7 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?