An alt's eq2ui file (which, I am assuming, yo are referring to a <CHARACTER>_<SERVER>_eq2_uisettings.ini file) has no bearing on the ability to use a custom UI. The main purpose for that file is to retain the positions (and other settings, such as opacity/transparency) of the various windows in the UI.
I'm guessing you are missing the required eq2.ini file that should be in your root EQ2 directory (
Instructions).