Also, incidentally, looking at the directory structure in Windows,
I've got a bunch of corrupted data on the drive. As Linux will not
let me do anything to the drive (nor does it show this data), and
Windows will not let me delete those files due to the names they're
showing up as (invalid syntax), I'm going to end up having to format
my drive it looks like.

Any suggestions as to how I can avoid this in the future? Because I'm
going to need to copy data back over it to get everything set back up,
and I'd rather not see it get corrupted like this again.

Don't format just yet! Unmount the thumb drive and, from a terminal run
the command

sudo fsck /dev/sd*1

(you need to replace the '*' with the letter assigned to the pendrive -
the only way I know to find this is through gparted, although there is
undoubtedly a better way of doing it). This will undoubtedly find (and
hopefully fix) quite a few errors on the drive.

As to why it unmounted in the first place?

Fsck returned that the drive was "good", but I still had the
undeletable corrupted data. Since I got most of my files backed up
off of it (I was filling it with music for a day trip), I'm not too
worried about loosing data.

Another question, unrelated to the thumbdrive - I just got a new mobo
on loan until I can buy my own. Since the new mobo means that I have
to reinstall my OS's (I dual-boot with Windows and Linux), I'm curious
as to any suggestions on how I should partition my Linux directory to
make reinstalls easier in the future. I've got 13gb set aside just
for the OS (already have a swap partition and /home on another drive),
so any suggestions would be appreciated, since I know in a few months
I'm going to be doing this again.

If you don't want to open gparted, just take a look
at the output from 'dmesg'. Usually there you can see
what disk letter and partition it assigned to the USB
flash drive.