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We encountered similar problems when we were hosted by Gamespy back in the day, culminating in a server crash that ultimately forced us to move to our current host. The first time the MySQL problems started to rear their ugly head since then was probably back in 2006 at the earliest, when we started getting more bots and spiders. Various fixes and workarounds have been developed since then and it seems the problems go away for a while but then pop up again and we're left looking for what else is problematic.
The more recent problems started around May, just before we put in the new design. Even so, most of the solutions we've tried since then have involved investigating/disabling aspects of the new design to see if they're the culprits or contributing to the problem but so far it's led to more dead ends. A more permanent solution is in sight, but is unfortunately taking a bit longer to implement than I was hoping for because part of the process is out of my hands. It's a bit more drastic but we shouldn't lose any data when we finally have the new solution in place.