It is unclear from your post whether or not the problem has been fixed.

In either case, it looks like a similar problem I had a while back when I dropped my laptop and caused the hard-disk to randomly become undetectable. This caused problems every now and then such as when saving the registry because the driver would tell my hard-disk to clear the old registry before writing the new one down, with hilarious consequences (as you can imagine) if it only half-succeeds.

From the problems you have been experiencing it looks like the Vista installation has become confused, perhaps because part of the bootsector became corrupted.

In such a case, chkdsk would notice that part of the bootmanager was broken, and would "fix" it, which merely recovers the file - it typically doesn't know where to put it, and will dump it somewhere obscure on the C: drive (grr).

It is then entirely probably that the Vista installation CD would not discover any installed operating system on that partition, but various other tools would notice particular windows system files that would represent a valid Vista installation. These problems could be compounded if your hard-disk is periodically playing up.

Under such circumstances, it's typically best to just reinstall the operating system (don't use the format option at the disk-selection screen and you won't lose all of your files). If you experience a couple of BSODs later on, or the problem reoccurs, then the problem is almost certainly a hardware fault, and you should look into getting your laptop or desktop computer professionally repaired.