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hey justin, .. i've seen this happen with bad queries. when i was experimenting with joins and making very complex queries, i looped mysql and it make mysql use 90% of the cpu. with that said, i'm guessing it's in your queries.
why not just post the queries that might be the problem? let us have a look at them... unless it's too much to post. i'll give it a try, but i can't guarantee that i can find the answer.
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