Actually, I think Lynne missed the part about this being a shared server. In fact you have no control over the server at all so don't bother going to the server configuration forum.
You haven't made it clear how many concurrent users you average, which is all that counts. The new default timeout in mysql 5 is a measly 20 seconds, which could be the whole problem. I know our host refuses to raise that limit to the recommended 180 or so.
My own year or so on Hostgator with sometimes as many as FIVE concurrent users on a shared server would often lead to server errors. Tech support always said everything was working normally.
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