As I understand it (and I may be wrong), MM4 has consolidated the locations where Extensions, Plugins, Scripts are now stored. It is all stored in "C:\Users\XXX\AppData\Roaming\MediaMonkey\" now. Any files stored elsewhere are remnants of MM3 and/or a script that is still not been updated for MM4.
Basically what I ended up doing was leaving all of the folder options unchecked in Backup Settings, and simply point my "Other Folder" to my AppData Roaming folder. That seems to catch everything. At least I think so.
This is what it looks like.