A number of display issues after upgrade (templates WERE reverted)

[ConfusedCartman]

I upgraded my forum software from 4.0.3 to 4.0.5, and there are now a number of issues with the site that I have never encountered before. PM display is broken for some reason, even though all relevant templates for that were reverted. Pagination (just the display - URL access still functions) is gone in search results (templates were also reverted), as if the plugin isn't being declared correctly or something. I've tried disabling all hooks via config.php, and it didn't fix any of these issues, so I know it's not an incompatibility causing the problem. I've even tried the default style, with no custom edits - same issue. I don't know what the problem is, but I'd be very grateful if someone could help me track it down.