Dual Operating Systems File Corruption?

I have Win7 on NTFS, Ubuntu 10.04 on EXT4 and a third partition for general data with both operating systems can access.The third, shared partition is in FAT32.I have had this set up for years with no problems. Recently, I have found that files that I use, move, etc on my Ubuntu sometimes become corrupted. It is very occasional but is occurring more regularly. I use many files (obviously) but only a fraction of those appear to suffer with the problems. The files are generally left irrecoverably corrupted. It is only files that are stored on the shared FAT partition that become corrupted.All partitions are on the same drive.

To solve the problem, I reboot into Windows and sometimes CHKDSK does it's thing and sorts it all out. However, when CHKDSK does not run, the files are irrecoverably gone. CHKDSK says there are orphaned files, removes and recovers them. Sometimes, a file which has been deleted on on Ubuntu may then cause CHKDSK to scan, find and remove the file (or more particularly, sets all affected sectors to null). I can't quite place the error. Possibly in a ageing and failing Hard Drive? The Laptop is circa 3 years old-ish. I would say that combining file systems is an invitation for trouble - but genuinely I have never had any problems with it before. Sometimes I access Ubuntu when Windows is suspended which I feel may cause Read/Write collisions at OS level but if that is the case, surely it should prevent me accessing the file, rather than permit it and then treat the sectors as bad?