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It is hard to say what is the root cause of the problem, my guess is the table level lock in MySQL. One request locka a table for too long and blocks other requests, so requests are queued up at the front end server, which causes the high load. You can try some vbulletin hacks that minimize table lock problem if you haven't, I might be wrong on this though.
Other things you can try is to upgrade PHP to 4.4.1 along with the ionCube loader/accelerator.
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