I usually add MSE after both WSUSo and the other progs I add myself, but this time I am only doing a windows (XP) update, so I figured I would add MSE to the WSUSo routine.
I'm not sure if it's connected, but I think MSE is at least a factor. I had the CPU running at 100% for 15 minutes while missing updates were listed. I've never had that happen before. MSE does a lot of initializing and updating right after being installed. I believe it would be best to reserve it for last in the WSUSo queue so it doesn't interfere with everything else going on.