Thomanji:
It sounds like you have it setup pretty well. No easy answers here. Looks like we'll have to do some real thinking. LOL
The first thing that must be done is to isolate where this query is being launched from. Here's a couple of other things to check. Does the page that won't load execute the query you listed in your original post or is it coming from somewhere else? If it's part of the page, does commenting it out cause the page to run? If you try running just the query in MySQL Admin or other tool, how long does it take to execute?
Definitely check for events and scheduled jobs running in the database. Also, events were a new (beta) feature in mySQL version 5. It could be an issue with proper running of events if they are part of your application.
AielloJ