This one is a doozy. 2009 car will communicate with every single OBD scan tool I've been able to find, but when I bring it in for inspection the state machine comes back with a communication error.
The only plausible cause for this is the fact that I recently removed a poorly installed remote start which required a bus line to be reconnected to the immobilizer/key recognition module. This wire was cut and intercepted, so I soldered the ends back together. I know the solder is solid because everything in the car works perfectly, and when a scan tool is connected live data can be read without a hitch.

I'm at a loss as to what else to do now, and am looking for help.

 

Can you carry out a network test using other scan tools?

 

Not sure what you mean? A network test?

 

On quality scan tools you can carry out a network test of all the modules sharing the Can network. This can tell if the wiring modification is to blame.

 

Well I have a tool with which I can scan all the separate modules, and I've seen an error for HS-can bus, which is I believe the wire I was messing with. However, the communication issue between modules within the car isn't a consistent issue, it seems that once in a while there's a hiccup that disturbs the communication and causes the bus to fail across the board for a split second.

Only 2 wires were cut, the RX bus line from they keyless entry module, and the black wire on the brake switch, not a ground but a signal return to the KEM. Using my scanner I can read codes from the KEM as well as live data without a hitch. The physical connector seemed to have a few pins pushed up a bit, so I pushed them back out. Hopefully this helps, but as with everything I've done so far it's a complete shot in the dark.
It's really hard to diagnose an issue that occurs only with the NYS inspection machine, since that isn't something you can just use in your free time.

 

I managed to get it to communicate. It turned out that the issue was the physical OBD port itself, and because one of the sockets has slightly backed out, the inspection machine wasn't able to communicate. It seems that the connector used on this machine has SLIGHTLY shorter pins than any other OBD scanner, and as such it was the only one to fail to communicate outright. Pushing the wires on the back while pushing the scanner onto the port (quite hard I might add) was enough to get solid communication.