Blame it on the patch, I did hehe.
Last patch some files were downloaded to the uifiles/default directory. If you have made mods and happen to be using a different dirname to load skins from now then your directory won't have those files. One of those files was EQUI_TextEntryWnd, which looks suspiciously like it would be the window used to enter text for the Rename Window command.
I would say to copy this new file from uifiles/default to your new folder but I don't think that will solve your problem by itself. There were other files patched also, including EQUI_Animations and EQUI. You could download these with no changes as long as you haven't changed them before and there should be no trouble at all. If you have changed them or downloaded new versions of them (Geddine's long target window for example changes the EQUI_Animations file) then it could be more difficult.
For a full list of files patched just lately go to:
http://www.eqgui.com//showthread.php?s=&threadid=388