I have a solution that seems to be working. This particular problem appears to be timer related.
With RHEL4 u.4 and the Tyan s2915, combined with two AMD Opteron 2220SE's, the kernel (2.6.9-42.0.8) was using pmtimer/TSC based timekeeping. This was not working correctly, see
The Tyan BIOS v101 has an option enable the HPET timer. Once this is enabled the kernel will choose the HPET by default bypassing the pmtimer.
The system is now stable as can be, knock on wood.
netllama was correct in stating this was a BIOS issue although I am stumped as to how it all relates to nvidia and kde/gnome etc.
Thanks again for all the help.