There's always a chance of anything corrupting your flash drive if you use shitty flash drives. Same goes for hard drives. Use quality materials and you're less likely to run into problems.
I've been running OS's from flash drives for a couple years now and I have yet to have a single corrupted flash drive.
Does Kingston 8GB Datatraveler G3 sounds shitty to you?
Also do you use ext2 or ext4 with yours that are running fine for a couple of years?
Because ext2 doesn't use journalling, thus much better suited for flash drives. While ext4, which is the default Ubuntu 11.04 file system is much more damaging to the drive.