The ECM controls the engine systems and certain other related systems like the electronic throttle, electronic shifting, etc. The VCM controls the Vehicle Stability System (VSS), which is made up of the Stability Control System, the Antilock Braking system, the Electronic Brake Distribution System, and the Traction Control System. The VSS is often referred to as "the Nanny" because it tries to not allow you to do certain things with the bike that would "get you into trouble". :sour: Both are located near the front of the bike. When necessary, the two modules communicate with each other electronically, via what BRP calls the CAN bus.
I was not aware that these two modules had different warranty coverage. If your Spyder is still covered under the BEST extendeded warranty, I'd give them a call and ask about it.