I have a machine that came with Windows 7 64bit on one hard drive (ssd). I installed Windows 7 using the OEM recovery disks on a second drive (ssd) and I am currently dual booting using the BIOS boot menu. In both Windows 7 installs all hard drives are mounted and visible to each other, so that I can share files between them.
The problem I experience is that several times already (in a short period of time) chkdsk runs when I switch between the the OS saying that there are problems that need to repair, which it does and then it boots fine. However, the last time I booted into Windows A it said that there is a problem with A's partition and it can't run chkdsk. I booted into Windows B, which ran chkdisk automatically and fixed A's partition, but A wouldn't load due to a blue screen. I ended up using some OEM repair tool which showed up in the Windows A boot menu and that fixed it.
My question is:
Is my setup wrong? Why am I seeing those chkdsk problems? One of my friends suggested that Windows B is overwriting Windows A's volume identifier which is causing it to get confused and visa-versa, but I can't find anything useful on the Internet?
P.S: I have ran numerous HDD diagnostic tools on both HDDs and they show no problems.