Do you know in what way they are out of compliance? I'm assuming they have the SMP and Patch agents, right? Have they received other patches? Have you staged the patches you feel they are out of compliance with? Have you made policies for those patches? Are they simply missing some systems or all systems? Have you checked to see if they show up in their policy configuration to be in the filters that should receive those patches?
I think there are some general patch troubleshooting guides in the KB - you might start there. Basically, as you can see from the questions I just posed, there are actually a wide variety of reasons for what you are seeing.
There is another 2 possible reasons not listed above, but until you rule out the ones above, the next too are, generally, moot. One, Nessus may be wrong (yes, it does happen) and two, we may be wrong (also happens). In the former of the two, there's little we can do about it. In the latter, you'll have to rule out the above options first, and then show us how our rules were incorrect compared to Nessus, or something like that. I know there are KB's about looking at the evaluation rules.
Anyway, that's a start. Let us know what you need from here.
Thanks!