This was originally a bug in the wiki about a year ago, but it was fixed by adding the BASE tag - you will see that this site has no problems with popups like that. Since the BASE tag is appearing as intended on your site, I'm a bit confused why it's not being used in Internet Explorer there (tested fine on Firefox and Google Chrome). I'm inclined to believe that one of the other scripts on the page is causing a conflict - possibly by resetting the base directive or erasing it entirely.
I would start by checking if disabling AdBrite or the NCode Resizer on wiki pages has a positive effect, since these are the only scripts I saw that we don't both run, unless you have modified the core vBulletin JS files.
If this isn't something you can do, but you can point me to the appropriate mods, I can try to reproduce this here.