FYI, I have ran almost 24 hours clean (I also disabled the restart of HTTP). Average CPU is holding around 10-15%, much better than the 50-60. Not pegging at 100% either. Another day and I will feel good with saying we are fixed.
Difference? One piece of info I exluded earlier was this server is a VMware VM running in a vShpere 5 environment. Previously, and it was fine running with 8.5 Domino/Traveler, I had 1 socket and 2 cores assigned to the VM. I upped the cores to 4 and have not had an issue since. I really do not think this has anything to do with VMware, given 2 cores was fine up to the point I upgraded to Domino 9/Traveler 9. I am OK staying at 4 cores if that is needed, however others should be aware if this occurs to them.