I too recently upgraded from TwonkyMusic (4.1) to TwonkyMedia 4.4.1.
Again, the hotkeys on the remote were no longer working with the upgrade, even though, as I had done with TwonkyMusic, I changed the names to Artists and Genres in the Music Tree, as detailed on this forum. But no luck, it didn't work.
Then, following Frank's idea, I did a few tweaks which I will detail here to benefit other MP-101 users.
I went to the Picture and Video trees and deleted all entries, since the MP-101 has no need for them, then saved changes as always required. Also, under Naming, I deleted any entry under All Pictures and All Videos as well as under Pictures and Videos. You must leave "Music" entered in the Music field.
Then I rebuilt the database and all was amazingly well!!!