Okay, I seemed to have stumbled on a fix... I went to Preferences/File Converters, unchecked MP3, AAC, and just for laughs, Flac, applied the changes, then went back in and re-checked Flac, applied the changes, and voila, I now have a full list of file formats available when I need to convert a file.
Obviously I have absolutely no idea why that would work, I'm just glad it did!