Well, it seems that certain combinations of flash drive, motherboard and FAT16 can end up with a corrupt drive after writing data to it. I've never experienced it myself, but I don't trust it too much. Besides, since we're stuck with USB1.1, it's faster for me to shuttle the files across the network anyway. Earlier versions of 4.0 and 4.1 had other issues with some drives, since the most recent updates though I haven't found a drive that didn't mount, including USB hard drives, memory card adaptors, flash drives etc.
Motherboard issues are another thing altogether - as was said here the XE is somewhat repairable - mine doesn't show any hardware-related issues, but the SE seems to be worse off by all accounts. You could always buy a compatible USB PCI card and use that, or some people have had some luck plugging a powered USB hub into the rear ports and just using that for flash drives instead of the ports on the machine.
