RT-Preempt Kernel patch fails to run SMP on two cores

I and other members of my Folding@Home team have been able to reproduce this issue on various distros.

After patching and building any post-2.6.26.8 kernel with the corresponding RT-Preempt Kernel patch (from Ingo Molnar and his development team) the current SMP Linux folding client 6.24 fails to run on multiple cores, instead running on only a single core. All vanilla kernel builds run the same client flawlessly. We have reproduced this on Ubuntu, Fedora and Gentoo.

The last kernel version that we were successfully able to run the client on was 2.6.26.8 and patch-2.6.26.8-rt16. Please note I am NOT referring to the linux-image-2.6.28-3-rt kernel in Synaptic (from the same development team) but a custom kernel built from the same sources.

I have used the same .config file to build the kernels for my machines, testing each vanilla kernel first, and then patching and recompiling with the same .config. In every case, the client starts, and then engages only one core of both my Opteron-185 and my Q6600, using the one core at 99% and the other(s) at 2%.

Others on my team have tested this on Core2 Quads and i7 Quads with similar results. I am not sure how or whether to file a bug report, because it is possible that we are missing some obscure option in the kernel config, although I believe the likelihood of that is small, since the .config runs fine on vanilla kernels. Can someone steer me in the direction of the right source for some help? Thanks.