Just reinstalled Altiris Deployment Solution 6.9 SP4 from scratch on a new server (new name and IP) with a new database. Installed it on VMware ESXi 4.1. Then pointed my old clients to the new server. Noticed that the CPU was running at 100% on the new server, and axengine.exe was the culprit.
I increased the VM to 2 CPUs, then 4 CPUs, and it was up to 75% CPU usage on 4 CPUs.
I figured out the problem, which was something with agent encryption. CPU was at 0% until I installed an agent and enabled its encryption on Production Agent Settings, Security tab, checked "Encrypt session communication with Deployment Agent". Then the CPU on the server started to spike. Didn't matter whether I had "Require encrypted session with any server" checked or not.
Uninstalled the agent from that machine (Win7 x64), then reinstalled it with no encryption set. My server CPU is staying at 0%.