ARMAX does sometimes take quite a while to load the codelist, even when it's a fairly short one (my codelist of about 10 games seems to take ARMAX about 45 seconds with no motion of the progress bar). Are you sure you waited long enough?
Also, make sure you use the ARMAX Max Memory program to delete codelist data from your memory card -- the built-in PS2 file browser cannot "see" the codelist file so it won't be able to delete it (if it shows anything at all, it usually calls it "corrupted data"). But be careful with this -- if you delete too many saves at once in MAX Memory then it can corrupt the entire memory card and force you to reformat it. It's best to stick to one at a time, and make sure that you've made backup copies of your saves beforehand.
Other than that, though, I think the best thing to do is to try a process of elimination. Try unticking all of your custom lists, first of all, and see if ARMAX can successfully load just the basic downloaded list (it's possible it won't -- CodeJunkies have been known to upload broken lists in the past, although they usually fix it fairly quickly, and usually they're broken in a way that makes MCM refuse to load them at all).
If it can successfully read the basic list, then try adding your custom lists in one by one until you find the list that it doesn't like. Then untick that one again and copy each of the games within to a new list one by one until it breaks again. Then try to work out what it is about that game's codes that ARMAX doesn't like. And don't forget to share it with the rest of us
