Your issue kind of sounds like a couple of different things to me cause I have noticed this prob in the past on certain things
Did you run DPC latency check to see if anything was spiking the system with X1 up and running?
Kind of sounds like something in the background running gimping up the memory locking up the system.
I have been able to make mine loose sound by messing with ProChannel or mem intensive Plugs when the transport is in motion. Indicators for me were the same. All meter moving, transport scrolling and all looked normal, just no sound. Have to close and relaunch X1 to get it back.
When you bring up SD3 from Track View on/from a track on the far left next to the track number, have you tried to reassign a program for the sounds?