If a focuser works properly through the focus program, it should work fine through CCDAutoPilot. If you are using temperature to determine when to focus, make sure you select the proper temperature source on the Focusing page.
Specific Hardware Notes
Optec Focuser: Be sure to turn off the Optec's temperature compensation. The focuser can not be remotely commanded if it is turned on. If temperature compensation is desirable, use CCDAutoPilot's internal temperature compensation routine.