MySQL performance drop with FC2 kernels

[N T]

I am seeing that performance using MySQL 4.1.7 drops by a significant
amount if I use a FC2 kernel (2.6.8-1.521smp or 2.6.9-1.6_FC2smp)
compared to running a stock 2.6.9 kernel downloaded from kernel.org.
The vanilla kernel was compiled using the i686-smp config that FC2
used. I see similar issues when running MySQL 4.0.xx. All MySQL
versions were installed from the RPMs available from
<http://www.mysql.com>.

The benchmark being used to measure performance was RUBiS
<http://rubis.objectweb.org/>. While vanilla 2.6.9 can service ~220
reqs/s, FC2's version of 2.6.9 can only deliver ~120 reqs/sec.

I have a Dell Poweredge with a hyperthreaded Pentium IV. However, I am
not sure what other information might be relevant to narrow this
problem. There was a thread on FedoraForum.org
<http://www.fedoraforum.org/forum/archive/index.php/t-20064.html>
about a similar problem but I did not see any resolution there.

Any ideas?

Thanks,
Niraj