I agree with your analysis - not a phrase I use every day here 
I guess the question is, if it is a problem of floating values, are there other lines that could/should be pulled up/down? Or, is there a way to regain control after the program basically stops running?
Good question. It is probably worth asking on the AdaFruit forum as my only experance of this chip is getting it to run in the stand alone mode MIDI mode and it looks like all other pins are right for that.
Sorry I could not be of more help.