We tracked the problem down to Net::MySQL which is being used by our mysqlPP driver. Switching from Version 0.9 back to 0.8 'fixed' our problem, which seems related to the way in which the module handles older (this database is running the v4.1.10 of MySQL) databases.
Comment on Re^4: DBI Access Denied with blank password
unless you have no compiler handy, I would heartily recommend switching from DBD::mysqlPP to DBD::mysql. It solved all my hanging/timing out/slowing down problems.