Sorry to bring this back up, but this is actually the exact trouble that I'm having! I feel like this thread is so close to giving me the answer, which is why I didn't want to create a new one.
I have tried your fix, gregrocker, but unfortunately it doesn't work...yet! I'm sure there's a way to make things right.
Let me get more into the specifics. I bought a laptop with a 500GB HDD with Windows 7 factory-installed there. I later added a bootable mini-PCIe 64GB SSD drive.
After having added the SSD, I ran an install of Win 7 with both drives plugged in and deleted all partitions from them, before installing Windows 7 on the SSD. Installed and booted well, only problem is that the "System Reserved" partition appeared on the 500GB HDD. If I try unplugging the 500GB, Windows 7 won't boot...
When I ran your fix, gregrocker, I made SSD OS partition active, and after the 3 repairs it placed the system back on the SSD, and let it boot correctly. BUT, when I plugged the 500GB HDD back in, the "System Reserved" partition that was still in there couldn't be deleted, as it was in use and active: the system had in fact booted again from that damn partition!
What I tried so far:
-Installing with 500GB HDD unplugged, which worked to get the "System Reserved" partition on the SSD. The 500GB was completely empty, but when I plugged it back in, the system would still not boot anymore! I ran a repair from disc which got the "System Reserved" partition back on the 500GB...
-Format 500GB HDD with one big partition taking up all the space. In that case, unable to make the System Reserved partition, Windows 7 very intelligently chose to make the whole 465GB partition an active system partition without an assigned letter. Wow, Windows 7 is really good
-I also tried running this fix
(fix number 3 was the closest). Didn't work...
I should specify that I run my disks in AHCI mode and that the 500GB HDD is on port 0, SSD being on port 3 (can't change that...).
Any answer would be greaty appreciated! Thanks in advance.