p.s. your description of the problem seems to match last night's observations on mount behaviour..
I had previously thought that somehow the tracking was being disabled on the mount when guiding was initiated, but I think it is more likely that the mount is executing an open looped move per your explanation above.
When I deliberately turn off tracking, the stars trail in the OPPOSITE direction to what I had been seeing previously when trying to guide.
So it is not that tracking is disabled, rather being overridden by open Move command..