I've spent the last day or so trying to narrow this issue down and think that I've gotten pretty close.
Whenever I transfer many small files, or single large files (anything that requires continuous write), the Fuze will begin transferring files (VERY slowly) and eventually freeze and unmount. Most of the time this results in corrupt files (or maybe even filesystem) which means the drive needs to be reformatted. This isn't such a big deal on the SD card, but the internal memory has to be reformatted using the Sansa firmware (and the Rockbox reinstalled). Either way, though, you're losing your stuff and you can't transfer much.
A single file or a few small files can be transfered, but it is incredibly slow. This is probably why I haven't noticed it so far as I usually just transfer a song or two here and there.
I've ruled out cable issues, sd card issues, and any other hardware related problems. I'm using Ubuntu 12.10... one possibility is that I installed the OS and have changed the MB since so it may not be built specifically for my MB. I plan on reinstalling the OS in the near future, so I will try this process again when that happens. But I don't think that is the problem as I have had no other issues with it, and for the following.
I've wiped the Fuze's internal memory and tried each prior release of Rockbox. This happens on 3.12, 3.11.2, and 3.11.
Finally I tried 3.10 which works great. Files transfer very fast without any issue at all.
(edit: Just discovered 3.10 is not working completely without issue... large files seem to cause the same problem. I'll have to try some more stuff later on.)
Has something changed 3.10 that could be causing this? Is this an issue I should report? If so, please let me know what other information I can help with (logs or anything).
Thanks to anyone for any suggestions.