Which CPU? Coldfire 1, 2, 3 or 4?
Assuming you're using something like an MCF51CN128, do you have RXEDGIE set properly?
13.3.5.2 Stop Mode OperationDuring all stop modes, clocks to the SCI module are halted....The receive input active edge detect circuit remains activein stop3 mode, but not in stop2. An active edge on thereceive input brings the CPU out of stop3 mode if theinterrupt is not masked (RXEDGIE = 1).