It won't rename .3gp files, I have to rename the extension to something else,
such as .avi, then back again. I thought I saw an option setting somewhere,
where I can specify what file extensions I want Filebot to consider. If it's
there I can't find it now. Help? Thank you.

You can open up FileBot.jar and open up the media.types config file.

But probably easier to just skip auto-matching. Just fetch episodelist in
Episodes panel, and then drag everything into "New Names" area. Should be an
easy-enough workaround till I fix this with next release.