Gregmang
I have the same issue with X3. It didn't exist with X2.
I have X3 and X2 on my home PC. They both do the Now Time marker thing.
It's worse in X3. It won't move in X3 until I stop moving the mouse. But only when the mouse is in Track View. If the cursor is outside the TV, no problem.
With X2 while cursor is in the TV the "Now Time" marker just jump every now and then.
But I get no glitches or snap, crackle, pops in X2 or X3 when this is happening. Even playing a 29trk (with minimal plugins) audio project.
Home PC Q6600 Quad Core @2.4g, 4gb DDR2 Ram, Win 8.1