I've been having this problem forever and just installed 2.1 hoping that it would finally be resolved and it's not.
Scenario:
Server 1 needs 3 updates via Manage | System Update
I check the boxes and go through the install. The install finishes and says it completed successfully.
I manually tell that server to refresh its inventory and then check software updates again and it still shows it needs the same updates. I closed OME and went back in and same thing.
I have verified that the updates did install but it's such a pain in the @ss to get OME to see that.
Does anyone have a surefire way of getting OME to properly see that updates were installed so it can properly update the Non-Compliant page? Soooo frustrating.