I'm using compiz 0.8.4 on Ubuntu 10.04 and I have the same problems.
Update Manager steals focus, as does every other application after
starting up while I'm working in another window.

I strongly second that "Personally I don't see any good reason to steal
focus, ever. It is quite simply rude and annoying."
(https://bugs.launchpad.net/ubuntu/+source/update-manager/+bug/373974)

As pointed out in https://bugs.launchpad.net/metacity/+bug/67476 this is
security risk.

-- 
Child Windows [of Synaptic/update manager] should remain in the same desktop as 
the parent window
https://bugs.launchpad.net/bugs/391479
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