I believe that stopping a plan is supposed to turn off tracking. The reasoning is that, left with no controlling software, tracking could eventually cause the scope to hit the tripod. Once you restart the plan, a goto, tracking, plate-solve and guiding all kick in. I was also surprised the first time I saw tracking get turned off, but it actually makes sense.
But, if tracking is getting turned off at other times, at random, that sounds like a legitimate problem. Send ZWO the logs for when it happens.
