I have a number of usb drives on my Ubuntu 8.04 system. Two are external hard
drives and one is an 8 GB usb pendrive. All are formatted with FAT32. I also
have a 20 GB external drive formatted with ext3. I can use all of the drives
from both Windows and Ubuntu without any problems, except the ext3 drive which
is only readable from Linux. In fact they also work from other distros that I
have installed: Sabayon, MEPIS, PCLOS and SUSE. I have used the same drives for
years.

The first thing that I would check is the usb drive itself. I would try to
retrieve any files off of them using whatever OS was able to read it and would
re-format the drive, in whatever OS you feel most comfortable. I would use a
format that is readable by all OSes, such as FAT 32. I would check the drive for
bad sectors if it is a conventional hard drive. If it is flash drive then I
would be a little leery about using it for anything important.

I am not sure about why this happened. Let us know if it happens again or if it
straightens itself out. If it doesn't we will attribute it to a ghost in the
machine. If it repeats try to pay attention to exactly what you did and report
it back to us.