Thats good news.
As for the popup box problem, I think the only one I can bring up as a guest is the ‘view edit history’ on a post. But that popup seems to be displaying fine. The only difference I can see between the standard ui-dialog box and the one on your theme is that you have yours set to position: absolute, which I believe we overwrite with position: fixed, but it shouldn’t change the size.
Is this happening on all popup boxes? including the edit post popup? or am I looking at one of the only ones that works OK? Still it shouldn’t matter as they all use the ui-dialog class.
I would suggest clearing browser cache if you have deactivated a plugin that was having an adverse effect, and if that doesn’t resolve it, try clearing the combined css/js cache in forum > toolbox > housekeeping