I can tell you that the Pentium D CPUs work fine with CentOS 3 and kernel 2.4.21-32.0.1.ELsmp. Presumably the newer kernels incorporate more support for these CPUs, possibly activating additional features not supported by earlier kernels. But they work fine with the older kernels.
Bug 147823, https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=147823, seems to describe the problem -- basically, there are/were issues with hyperthreading and dual-core processors where the machine would run slowly when hyperthreading was on. With hyperthreading off, the machine acted like it had two ``real'' processors and worked fine. There's supposed to be a fix in RHEL3 U6 (and presumably there's a similar bug for RHEL4 and an update for RHEL4 U2).
Claire