doctree - You have the scanner setup for a rebanded system, correct? And it's set to CC Only mode? If you have a second scanner handy, I suggest programming in all the system frequencies in conventional mode, lock out the active CC, and scan the others for activity while listening on the PRO-106 having the issues. If you start hearing conversations directly on the repeaters in conventional mode, but the 106 is not trunking, then something is clearly not right with the programming. If you're getting the same results in trunked and conventional mode, hearing only one side of the conversation, then it sounds like a much bigger issue beyond your control!
Are you sure you have all the control channel frequencies programmed?
A Motorola Type II system can have up to four CC's, only one of which can be active at any given time. Theoretically, a system can stay on the same CC forever, never switching to the other 3, but that's usually not the case. Anyways the point being, you really only need to have the active CC programmed at any given time, the other three are irrelevant. You would know right away if you didn't have the active CC programmed, because the scanner would simply not trunk track at all. Since the OP has indicated that he's getting TG activity, the problem is not the CC's but rather something else.