Make sure your mount is capable of responding to commands issued by CCDAutoPilot through the Telescope Control Program's automation interface. This can be verified by using the Test buttons. If those buttons don't have the desired result, there is no way CCDAutoPilot can cause those actions to happen. Check the mount driver software. Many times there is a later revision that may address some missing functionality.
Specific hardware notes
Gemini: To allow proper meridian flip operation, check the Safety Slew box on the Tracking and Guiding page. See Meridian Flip for details. Alternatively, on your Gemini controller, set the Goto Limit to exactly the meridian - 90 degrees.
Paramount GT1100: For the original Paramount, check Safety Slew on the Tracking and Guiding page. See Meridian Flip for details.