Again, this is using Gentoo's 4.1.8 version of mysql. It seems like people have been having good luck with 4.0.22, so maybe I'll try to (gasp) downgrade to that? Are there any other configuration switches I can try putting in my.cnf? Any other misc. ideas?

4.1.8 is still hard masked... I've been waiting for a few months now for 4.1 to go stable in portage so I can look into scripts that take advantage of mysqli. Unless you honestly need it, I'd hold back on 4.0.