Hi,
Firstly I have only just finished my bartop and am doing the same as you..getting the software sorted.
I am a complete newbie to front ends and mame really but I did solve a problem with config in maximus.I read something in these forums regarding the separate config that comes with maximus being rather buggy and the post said to use the ctrl P way of running config from inside maximus.
ie: open maximus then hit ctrl - p and try that..it sorted my problem with controllers so hope that helps.