Nope...that didn't do it...
Didn't think it would...the clean install didn't do it either...but I figured I'd try it again for fun
...
It really looks like it's basing the centering for those windows off a 1024x768 resolution. If you dig around in the xml files for the Default UI, there are quite a few that seem to reference 1024x768 still.
As well...the eq2_default has a cl_screensize of 1024x768 still...and it resets to that if you try and change it to 1280x1024...
Still weird hehe...