Brogan, to tell you the truth I'm not sure if it ever worked, but I did a separate install on my server to test it out and it's working on the separate install. So I guess we can rule out being a server thing..
My addons are:
Post Message Regex Replacer 1.0.0
The Happy Place 2.0.1
[8wayRun.Com] XenCarta (Wiki) 1.2.2
[8wayRun.Com] XenPorta (Portal) 1.2.3
I disabled all the addons and re uploaded the upgrade files as you mentioned and it's still not working :/