To MOB..Yes ECU's are interchangeable. I bought one on for my '09 off of ebay and had SISF flash it. It had to be setup for the bike with the KDS system he has. We used it to test his flash in the early stages last year. It is the same part number as the one in my '09. Zarticus was there with us. He would flash the spare and i would come up on the weekend swap it out and test it for a week. Giving him feed back in the process. 
Thank you for your response,
I never said an ECU could not be replaced or reflashed To function.
If you go back, and read thru this post, specifically the o/p's description of what took place, and my responses to what he described as actions taken by the dealership, you will find my responses were correct.
The ECU yo purchased off Ebay, had to have been the same year, or generation as your original to have the same part number....which you state. Is a 2009 bike.
Also, the ECU had to be flashed to your bike in order to function.
It clearly would not have been a 2015 ECU you got....
The o/P states he has a 2011, and they "stuck in one from a new bike on the showroom floor", which I assume would be a '15 or '16 model
He said nothing about them flashing it, nor do I think they would, as it was from a new bike....
Nor did they hook up a KDS to analyze the system, had they done that, they could have run diagnostics....which we have no feedback on.
My statements are also based on the differences on ECU and solid state relay modules between 2011 and 2015-16
2011 ecu is 21175-0368 can/usa or 21175-0369 Calif.
The relay box is 27002-0007
2015 ECU is 21175-0958 Can/USA or 21175-0959 Calif.
Relay unit is 27002-0025
SISF can further explain why what I described as being done by the dealership simply wasn't feasable, but I think if you read what I said, its understandable as why I said it.
I'm still awaiting some semblence of clarification from the o/p as to what the outcome is, once someone does actual diagnostics on the bike.
