I think I've found a solution to the problem some of us are having.
http://jira.phoenixviewer.com/browse/PHOE-3663
https://jira.secondlife.com/browse/SVC-7540
It appears this is a sever issue that only effects some accounts, particularly those that have an empty mute list.
It worked for me, as soon as i hit mute an entire weeks worth of offline messages came flooding in.