These might be issues with my hardware but I don't see this happening with other DAWs. They only happen the first time I run Sonar after starting my computer.
1. Mackie Control - Fires up, faders move, counters count, indicators indicate. After a while none of the controls or buttons work but the indicators still do. Restarting Sonar fixes the problem and it does not reoccur until the machine is restarted again.
 

As nobody has responded to this thread in three week in the problem reports forum and right now looks like an issue away from Sonar I'll move this to the Sonar forums. If there ends up being a reproducible bug I'll pop it back.