Hello John,
I'm a pretty heavy PEM2 user, and a 600 arc min error is a reporting error if you truly think you are close to alignment. Sandy may be right over the translation being in seconds instead. Correctly stated too, 600 sec out is still huge.
I've often seen PEMPRO blamed when in fact the user made a simple setup error. When you don't know, it's not easy to see the error made. So try reading again the manual set up steps per your mount type. Depending on your focal length, you definitely could try alignmaster, but alignmaster will never provide the same alignment accuracy as PEM. Longer focal lengths will benefit from a good understanding of PEMPRO2.
I use PEM for remote and observatory setups, and I can achieve a 0.1 arc min error result in about 15-25mins max. An AP mount certainly helps, but with a G11, I can do it in the same time frame.
Two recommendations, leave out the black screen/ move star routine in PEM for both RA and DEC. Just use the graph/ plot screens; these are all you need to complete to achieve an excellent alignment. I also recommend at least two iterations to get reasonable accuracy (0.1 arc min error). Lastly, make a cheat sheet per adjustment that helps you work out the amount of revolutions of your mounts knobs per arc minute of error, and the direction of rotation needed to fix the east, west, up, download error corrections.
Good luck!
Steve