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XOOPS.org runs multiple sites from a single db, and our PM table alone is about 70-100MB big at any given time... But we're not on a shared server, but run our own dedicated server.
My guess is that the database server is having trouble with the load, and not per se caused by you alone. Try to get an idea of the number of queries generated (in the MySQL debug window), if that is high, you need to do more optimising, if it's reasonable (depending on what you're trying to load it can be 20 queries per page), you know it's the server itself that's the bottleneck.
Herko