Had the same problem. Got skills window to work by doing the following.
Open up the eq2ui.xml in the default directory
Open up the eq2ui.xml in the custom directory
Compare the two (I used a spreadsheet). Add all the includes in to the eq2ui.xml custom directory that were in default directory. I didn't delete anything from the custom directory or the default directory versions of eq2ui.xml rather I just made sure all the ones in the default directory version were also included in the custom directory version.
Situation may vary depending upon what interface mods you have. In general though if the default eq2ui references some includes - then the custom eq2ui should also reference the same includes and maybe a few more.
A simplified example:
If Default directory eq2ui.xml contains:
<include>eq2ui_arenachampions.xml</include>
<include>_FetishStyles.xml</include>
And Custom Directory eq2ui.xml contains only:
<include>_FetishStyles.xml</include>
Then modify the custom directory eq2ui.xml to have both:
<include>eq2ui_arenachampions.xml</include>
<include>_FetishStyles.xml</include>
Well that was my attempt at an explaination ;-)
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