Windows 7: Windows is not installed on the drive from which it boots!?

I have 2 HDD, Disk0 and Disk1.
Disk0 is supposed to have my personal data, Disk1 the OS.
Disk0 has 3 partitions (H:/ I:/ J:/ ) and Disk1 has 3 partitions too (C:/ D:/ E:/ ).

One month ago I installed Win7 but erased my Disk0 by mistake and probably (very unlikely though! see below) started installing on there when I realized something looked wrong, canceled, then formatted Disk1 and installed there, on the first partition (I blame the badly designed Windows installer, Linux does it better).

Fortunately, I recovered my data from Disk0 (only partition tables must have got wiped out) after Win7 finished installing on Disk1 with a recovery tool.

I'm about to format Disk0 now (at least the first partition) but I noticed something weird on my Disk0 (data) hard drive.
I have system files, of which creation dates match the day I installed Win7 (and recovered my partitions too).


Note: disregard found.000, that's a file chkdsk must have created back when I used WinXP or something.
Note2: columns are "Date modified" and "Date Created", YY/MM/DD

I'm new to Win7 but I'm guessing these system files I see here should be on my System drive, not another drive, right?

Here is what I have on my C:/ where Win7 is installed:


Am I missing some (hidden) system files there?

Here is what I have in the Disk Manager:


I am confused. H:/ is marked as "System", which shouldn't be.


I am afraid that formatting H:/ might prevent me from booting anymore.
In such a case, will I have to either:
1) format C:/ and re-install Win7 ?
2) use recovery console and repair from there ?

The second solution would be fine by me since my Win7 installation DVD is on a USB drive (I installed from there).

As a side note, I am super confused as why one drive (SATA) is Disk1 and the other (IDE) is Disk0. I had to fiddle in my BIOS to end up booting on the right one (which I suspect is Disk0!). If I ever had to remove my IDE HDD, would I end up not being able to boot Win7?


Remark: I got suspicious of that when trying to encrypt my system drive with TrueCrypt and TC says it couldn't handle a system that "does not appear to be installed on the drive from which it boots".


---------------- SOLUTION --------------
* I disconnected my IDE cable.
* Reboot then set my USB key as HDD to boot on
* Started windows 7 installation process which immediately found the error and started fixing it, then ask for reboot.
* Second reboot, then second repair which I had to select in the recovery environment menu this time. Error got fixed again.
* Reconnected my IDE HDD.
* Re-set my usual boot configuration in BIOS (first drive being my SATA holding C:/, second drive being my IDE holding H:/ )
* Works fine! Thank you!

Disk 0 always gets the bootmgr
It's been a source of many complaints.
The only way around it is to make sure the disk you are putting windows on is in the disk 0 position or the only drive installed at the time of the format.

As your HD set up is about the same, have look at my post here:
Follow this base tutorial:
Help me get windows 7 to boot (again)

Ouch. This is worse than I thought. Another poor design decision by the Microsoft engineers? >:(
Are they even aware of that problem? (I sure hope so)

Thanks for the replies, I'll follow that tutorial and keep this updated.

Will this be a problem if I keep the current boot loader on my second HDD though (my current Disk0)? (probably a stupid question, if I choose to boot on Disk1 in the BIOS, right?)

What MS problem?

I was referring to this:

Perhaps not an MS problem? (I have no clue of what I'm talking about haha)
It's alright, I'll get over it. This is not like there is no way around this after all. Thanks again. :)

It is always best to install to Disk 0.

I agree. Actually, if I were able to tell which was which or even change that at Win7 installation time, I would have. I am fairly sure that my "OS drive" was Disk0 under WinXP, then ended up being Disk1 eventually, but I could be wrong.

Is there any limitation that would justify having bootmgr ending up on Disk0 whatever you do? I don't understand why it doesn't write it to the drive I'm installing the OS to, or at least give the user a choice somewhere.

Boot files are install to the first HD drive.
Which is also the first HD Drive, pluged in the first SATA port on the MOBO.
Showing in Windows as Disk0.

My current Disk0 is actually an IDE HDD (my MOBO is an ASUSP5E and there is some sort of mini-IDE driver starting after POST which detect my IDE drive accordingly). Disk1 is my only SATA HDD.