
I'm not sure your amp is at fault. Are the two connected by digital link or analogue? If the Sky+->TV link is in analogue and the Sky+->Yamaha is in digital, then it's a problem with the digital connection. The Sky+'s digital output and the analogue ones run along different lines at output and one could be off and not cause problems in the other.
I suspect the Sky+ box has problems. Is it a problem that resets itself after a few seconds? If so, it's a muting issue; if not, it's the digital output failing to lock on in certain modes. If the amp was randomly losing digital lock, the amp might be at fault, but it sounds like the Sky+ box has gone all crazy.
The words 'get a new one from Sky' spring to mind.