Have a look at it in GParted (which you might have to install first). It'll tell you if something's screwy with the partitions.
If so, the situation isn't good. You can use
dd to make a backup in case you figure out a way to recover the data, changing
sdx to the correct device and the
of= filename to your desired backup image name:
dd if=/dev/sdx of=/output/file.img
Basically, though, your partition table is probably corrupted. The only thing I know to do, absent some specialized tools which may or may not exist, is to delete the partition table and create a new partition(s). Of course, doing this will completely erase your flash drive; hence the backup I mentioned above.