Sorry, mixed up my GTO's and CP's...it is an older GTO2 mount with an upgraded CP4 chip.
It really appears to me to be that somehow PHD2 (and ASIAir guiding - which borrows from PHD2) is sending something to the AP900 controller that turns off or stalls the tracking.
Before I engage guiding, I can look at/image stars in 3-5 second loops for focusing and framing up and they stay tight and no position change.
As soon as I attempt to start Cal or Guiding from PHD2 or ASIAir, AP900 tracking stops, as confirmed when I again look at the images loops in focusing or previewing and the stars are trailed and moving. My target of interest quickly moves off frame.
Even with PHD2 stopped, I need to cycle through the Rate control on the AP900 hand set and reset to SID rate and the mount begins to track again. Otherwise mount tracking stays disabled.
I'll try Bryan's key pad testing suggestion. I typically use either the AP900 hand controller, but mostly have been using the ASIAir for goto's and slewing/manual jogging..