You're right. SGP will do it for you but it opens you up to the problems you're having. Your other choice is to speed up the number of steps it is taking to get a good calibration. In addition, you don't know how much backlash is in your system and that can delay it as well.
I think it's in the manual and it's been highlighted by Ken/Jared in the past, it is recommended to do calibration manually in PHD.