Astrodan,
Thanks for the advice. Unfortunately, it does not solve the problem. Close, but no cigar... My AP900GTO-CP2 with the E1 ROM chip onboard doe indeed allow for external initialization. I invoked that option on the keypad as you suggested and restarted the mount. Sure enough, it came up saying it was waiting for the external program. At that point I continued with the procedure you describe, following your instructions to the letter. While this does get the telescope cross hair above the horizon, it is still no where near where I expect it, i.e., due North at or just above the horizon (Park 1). Instead, it show up just under the bowl of the Big Dipper AKA Ursa Major. If I ask the scope to slew to, say, Polaris, it goes off in some completely inappropriate direction. If Park the mount back to position 1, it slews to a spot that appears to be where the cross hair first showed up, i.e., scope of the east side of the pier (rather than on the West) and about 10 degrees above the horizon.
Clearly, something is amiss with the initialization of the mount. I'm inclined to believe it has something to do with the longitude setting. I'm in California, USA, so my longitude is -121:53:1 or 121:53:1 W. If I try entering a negative number for longitude, it fails saying lat or long missing or incorrect. If I add 'W' or '+W' as a suffix, it produces the same results I described above. I tried doing a 'warm' initialization with AUTO CONNECT set to "NO" and got similar, but slightly farther off results.
Now I've considered the possibility that being a CP2 controller and running the E1 ROM revision might be at the root of this, but back under Windose, programs like Stellarium, The SkyX, Maxim DL, PEMPro, all interact with the mount in the expected manner with no need to makes special adjustments for the controller type or the ROM version.