One thought I had on this... I am currently using a very old PHP version (5.2.17) for the benefit of the 1.3.8a installation on this server. Maybe when I can migrate to the 1.5.5e site and upgrade my PHP version that could have an effect?

Also when I look in Tools -> Server/Version Info I do see: "MySQL Slow Query Log Status: On" and "MySQL Slow Query Log File: web-slow.log" but I can't seem to find that web-slow.log file anywhere.