Ryan:
There are a good number of ways to make MySQL cause high swap usage. It would be difficult to know where to start without seeing your SHOW STATUS/SHOW VARIABLES and the query log. Also, what happens with the memory footprint of the mysqld process?
Before going any further, I would also recommend export LD_ASSUME_KERNEL=2.4.1 in mysqld_safe to turn off NPTL threads.
-- Sasha Pachev AskSasha Linux Consulting http://www.asksasha.com
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