Rule #1 - Be Patient - Rule #2 - Don't ask when, if you don't contribute - Rule #3 - You have coding skills - LinuxMCE's small brother is available: http://www.agocontrol.com
1) Set max number of jobs to 2. The CPU is dual core and has hyperthreading enabled, and it handles this without flinching. 2) Enable the ""experimental speedup of commercial detection" option. With those two settings, I've more than tripled my commercial flagging throughput.