A better solution will be in place once one is found. I've been working on writing my own vBulletin-compliant initializer for PHXCMS, but so far it's not working 100% correctly. The problem with including some vBulletin PHP files in the main site is that I am not sure it's allowed per the vBulletin license and it would also add bloat to PHXCMS that would increase server load and page load times.
Well for what it's worth I still think that's a bug, even if intentional.
The ad tag is changed back to its original state now. To anyone that encountered the problem, could you please test to see if you still get the wide leaderboard in the skyscraper spot?