I thought you disabled your plugins? There are several lines in there regarding the chatbox, autoreply and thanks mod. I don't think those are your problem, but you did say you disabled your plugins and so those shouldn't be in there.
You said you have a VPN so you have access to modify php and mysql settings? If so, then you should post over in the Server Configuration forum at vb.com and see if George can help optimize your server.
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