I have a bit of an odd situation and this seems similar to the following (unsolved) post: http://ubuntuforums.org/showthread.php?t=857036 (I'll point a link in that thread to this..)
I have a laptop with a large (500GB) internal hard drive; this was partitioned to include a partition for Vista (NTFS), a partition for Ubuntu (EXT3) and a 'data' partition (NTFS). This was a new build on a new laptop with Hardy Heron 8.04; previous laptop worked perfectly like this and I was able to share data between Vista and Ubuntu by writing to the DATA partition (D: drive in Windows).
I booted into Vista a few weeks ago and, on booting, windows stated it needed to ru checkdisk on D: and this reported no errors. On logging into windows, found that the 'D: drive', although visible, was no longer accessible (message 'Drive not accessible') but, on booting into Ubuntu, get message 'disk needs to be checked for consistency'... completes, get into ubuntu and it can access/ read it all perfectly. Weird....?
It get weirder..!
I also have an external hard drive (500GB). Two partitions, one NTFS, the other FAT32. Accessible perfectly well between Windows and Ubuntu - but no longer. Ubuntu can see both perfectly, read, write no problems. Attach the drive when booted into Vista (or XP on my second laptop) and same result - 'The drive has malfunctioned' and the drive is inaccessible.
So I reformat the FAT32 partition in Vista - it's fine. Reboot into Vista, still fine. Drop a test text file into it - no problem. Reboot again into Vista - still works fine. Disconnect the drive, boot into Vista, connect the drive - perfect. Reboot into Ubuntu, open the test text file, make a change, save the change to the drive, shut down Ubuntu. Reboot into Vista - drive no longer accessible. Same behaviour regardless of whether I access a FAT32 or NTFS partition - once Ubuntu has had a touch, Windows can no longer access the drive. Most frustrating!
Any ideas on what on earth is going on???! I've trawled the forums but am no closer to finding a resolution...