I've been seeing this triangle-shaped indicator:
Telling me the following information:
"The update information is outdated. This may be caused by network problems or by a repository that is no longer available. Please update manually by selecting 'Show Updated' from the indicator menu, and watching for any failing repositories. "
The Software Updater tells me the system is up-to-date.
As a final note, the indicator seems to go on and off. At first it dissipated without me doing nothing. Then it came back.