When I looked into it a while ago, there was a statement on the website saying essentially that you might not get back the same ECU that you send in. That was enough to scare me off - you need to pair the ECU to the immobilizer. I tried to get a US "altitude sickness" ECU to work with my Canadian bike and it would not work. I had to buy a Canadian ECU to fix the issue. A Canadian ECU can also not be re-paired to another immobilizer after the first pairing.
See, now THAT is kind of a critical detail -- but one I have not seen mentioned anywhere or fully thought through myself. As soon as I read it I had one of those slap-yourself-in-the-forehead "DUH!" moments. Thanks!
Odd you could not get the US ECU to work though. I seem to recall Europeans buying US ECUs to bypass failed immobilizers and lost red keys instead of paying the Yamarobber an arm, leg and first-born child. (Comments attributed to Ivan in the thread referenced by RossKean state the US ECU has the immobilizer function, but disabled.)
Looking at the wiring diagram, there are 6 wires to the immobilizer unit -- power, backup power, ground, optional alarm, flashy light and one mysterious wire that goes to both ECU and multi-function display (ie: dash). My guess is that is a communications line, possibly CANbus or similar.
Now my curiosity is aroused: does the dash play a role? Never heard of that but Ivan says the CO compensation numbers are stored there. The Gen I will start with the dash disconnected, I wonder if the immobilizer bikes will? Or maybe your US ECU was defective -- one of those eBay "as-is" scams, perhaps?