Just a quick note to hopefully save someone from suffering the same problems that I am right now.
I've had all sorts of problems with my Windows 7 install - programs going missing, folders denying me access, firefox refusing to load, Steam going mental, and it seemed that the problem was related to disk corruption. CHKDSK keeps deleting index entries, but not getting anywhere, just cycling over and over again. Today it was complaining that it needed to fix the MFT bitmap, but was unable to owing to a lack of disk space, which is complete rubbish.
It seems that a lot of people have had this issue, and the common factor is Acronis, so consider yourselves warned
It may be possible that if you partition with acronis, but format it with the Windows 7 CD it will be okay, but I'm not sure about that.