it sounds to me that your USB drives are clonking out on you... cheapy drives will sometimes crap out under heavy sustained writes. Writes are tough on flash memory (USB drives) but reads are much easier.
I've had flash drives heat up a ton, stop being recognized by the OS, report wrong capacity, etc all from trying to write too much data at once to it. The solution, unfortunately usually is "Get a better flash drive". Nice ones from Kingston and Patriot are my favorites usually.
As far as trying to repair your current ones... unfortunately there might not be much that can be done. Standard mechanical hard drives can be low-level formatted (write all 1's or 0's to the entire volume then do format new partition and filesystem). This would be murder on a flash drive though... and might just kill it or get the same result you have now.
If you want, you can try using something like GParted to examine and see if the usb drives are salvageable. It has a bootable cd version as well as an installable version (if your on linux). It will let you destroy and create new partitions on the usb drives outside of windows and might be just what they need.