Brett,
I'm using filter focus offsets with my Atlas focuser under Maxim and I didn't do anything obviously different to you. I just set up the focus offsets and so long as the focuser is connected it moves when I change filters. The Atlas is quite loud when it moves, so it's pretty obvious that it is working.
Have you looked in the Maxim log files? There might be some hints about what is going on in there. You could also try asking on the Maxim group:
http://tech.groups.yahoo.com/group/MaxImDL/
Cheers,
Rick.