Bob,
I am in the same boat as you are. I have about 1700 songs in Songbook+ and it works as you mention, it goes from registrations to sheet music, and the other way around too. I find that after I shut down and come back later on to play again the links don't work until I restart MIDI. If you notice the MIDI Indicator on the top middle of the page, try playing a few notes on the keyboard and see if the indicator flashes each time you hit a key. If not click on MIDI and from the drop down select Restart MIDI. This will usually get you working again. I am hooked up wirelessly not using the BT01's. I don't know if that makes a difference.
Hope this helps!
Rick D.