After much experimentation, we found the right combination of configure options to get MySQL and Perl DBD::mysql to work correctly on a Red Hat Enterprise 3 box. We were getting some segmentation faults on the binary after switching to a custom kernel. It appears that BIND and MySQL, and probably other apps, are relying on something particular in the Red Hat kernel. We solved this by recompiling BIND and MySQL. Here is the configure statement for MySQL 4.1.13:

./configure --prefix=/usr/local --sysconfdir=/etc --libexecdir=/usr/local/sbin --with-unix-socket-path=/var/lib/mysql/mysql.sock --without-debug --without-bench --without-readline --with-mysqld-ldflags=-all-static