jackofalltrades

Ok, so I have a full 06' GTO swap. I built my own harness and am capable of pulling the VIN, make/model and DTC's using a $200 store bought scan tool. That tells me the coms work. It tells me there is a TCM com failure which I know I need to have the NEW TCM matched. So I took it to the dealer to flash it and the mechanic says his TECH2 system can't talk to the entire system at all.
I'm now at a loss. How can my cheap-o unit work when a $2000 system won't?
Any help?