I'm having the same issues with BottomBar Config not doing anything (as well as AutoAttackCalc and the Connection+FPS info). I have no files set to ignore. Since you ask about eq2ui_custom.xml, here is what's in mine:
<?xml version="1.0" encoding="utf-8"?>
<Page IgnoreTab="false" ismodule="true" Name="Custom" PackSize="1,1" PackSizeProp="0002/0003,0002/0003" ScrollExtent="1024,768" Size="1024,768" Visible="false">
<include>_ProfitUI_custom.xml</include>
</Page>
<Namespace Name="ProfitUI_Styles">
<include>_ProfitUI_Styles.xml</include>
</Namespace>
I haven't tried copying anything from ProfitUI_Custom to eq2ui_custom.
The bottom bar appears normally. I just can't call up the config tool.
-= Therendil =-