I don't understand why you are having so much trouble with it. Maybe it's just not doing what you think it should. But as it stands there are three options to select atmas. The usual way, an option to apply the last used atmas selected from the usual way, and an option to choose an atma set from your most recent selected atmas.

I'm constantly changing between NIN BLM THF MNK DRK and have no problem keeping the atma list maintained. If you want to use the option of "last used atma" then you have to choose them from the usual way. Most times I am able to keep my BLM atams as the last used atmas selected from the usual way and keep my melee atams in the recently selected atmas list.

The only thing I could see that would benefit from an adjustment would be to allow 2-4 more atmas stored in the "recently selected atmas" selection category.