New HC-PIO board didn't do the trick. Removed the traveler wires from the input terminals where my phantom calls are latching, calls still latch.

Got a good guy (James) from MCE technical support. After lots of poking around he suggested the same things that were mentioned here and by others I work with.

He had me check Bus 2 from controller to controller (ST2A to ST2B) in the group controller, they should read 60VAC or less between each other. I read 120VAC between the two, this indicates that the cars are out of phase with each other. This issue normally shows itself upon start up, apparently it can cause all kinds of oddball problems such as mine.

I ran out of time and didn't have the correct ring terminals with me today. When I go back Monday, I'll have to swap two legs feeding my main transformer until the cars read in phase. If this doesn't fix my issue, tech support suggested changing the MCCGDP board. I am going to order the board anyway.