Hey Mark, I'm not familiar enough with that Boss box to give you all the answers, but I can confirm that MIDI loop control works great in Touch 2 on the latest firmware (build 61). I just tested it out using Max MSP as my source and the following MIDI CC's work as intended:
CC 44 Value 0 = Play button CC 44 Value 1 = Record button CC 44 Value 2 = Stop playback CC 44 Value 3 = Undo CC 44 Value 6 = Lengthen 2X CC 44 Value 10 = Clear CC 44 Value 26 = Erase CC 44 Value 27 = Reverse playback
And a couple other things to confirm... If you go into the "Setup" menu, tab over to the "Loop" tab, and there's a parameter there called "MIDI Control" that should be set to on. With that, also check your MIDI channel on the "MIDI" tab and make sure your Touch 2 and Boss are speaking on the same channel. Hopefully that's helpful!