I had a very similar problem and was caused by creating a Dec-arc tracking model that did not provide enough data points to be used as a pointing model.  Didn't realize it would be an issue and had the "Use Pointing Model" box checked.  When a flip occurred and it actually started pointing in a wrong direction.  The rig ended up trying to do plate solves pointed at the ground.  I was standing next to it watching.  At least that problem was solved by unchecking the pointing model box.  Just one cause with a similar sounding outcome.  No idea if it's the same circumstances as yours.