I had the same issue. Make sure you take out any modified map UI and the EQUI_EQMAINWnd.xml if you have that one customized as well. Those are the 2 things that was causing the UI I made to reset back to default.
On that note, anyone know what they did with the "EQ/SC" UI piece? It use to be the EQMainWnd, but from the looks of it when I open up the default, that is no longer the case. And I would like my "small" EQ/SC buttons back.
~*~ Eyes are the windows into one's soul, Dreams are the windows into one's desires ~*~