I'm pretty sure I have posted about this somewhere before, but at the moment I really don't have enough time to fix the issue. I've already spent a fair bit of time looking at what changed when we upgraded and tried some fixes, but to no avail. I'm not intricately familiar with the changes that were made to the wiki software, and I've found little to help me migrate the system we had to the new version.
Sorry that that's probably not the answer you wanted to hear, but I really haven't had the time to look into it any further than I already have.