Maybe there is something wrong with the bone naming convention...the plugin needs "right" or "left" in the names.
I haven't had that happen, but it could also be because of the bone naming convention used..."r" and "l" wouldn't mean anything to the plugin, but "right", "Right", "RIGHT" would.
That would be more a question for Robert...I haven't done as much messing with TSM2. I would think the last thing would be flipping the bones before running the Rigger, but I could be wrong.
Hope that helps.