I have a main toon. I setup his profile in FuBar, and copied it to a toon I am leveling. If I make changes to the lower level toon (add experiencefu or something) the changes effect the main too. BOTH are set to their own profile.
Some of the ACE addons have their own Profile setting, while others do not.
If I choose, e.g. MyChar @ MyRealm profile in the fubar settings. I think I'm fine. But if I look at options of the addons sometimes there's an options "profile". By choosing this profile you'll probably see that it's set to default.
The inconsistency might be the cause of it. I've tried to change the addons with their own profile setting to MyChar @ MyRealm but I didn't have time to test if it worked as intended. But if this is the case of the profile problems it's up to the FuBar addons/extentions to implement the profiling into the FuBar when it exists - as it should be.