It seems this thread died before a resolution was posted, but I am having a similar problem. I have just built an EPO 4.0 server and currently have 18 servers being looked after by it. They are all running EPO Agent 3.6.0.569 and VirusScan Enterprise 8.5.0.781 patch 6, current DAT is 5352. Now I only have 1 policy running (atm) which seems to be working OK, but the update task is not running on 2 out of the 18 machines, and I cannot see why, if I run the update manually its fine, it goes to the right server and finds the updates.
Help! shout if there is more info I can provide.
Cheers
Steve