I sorta have the same problem, though not (primarily) with SMS, but with Skype conversations.

I would get notifications about incoming messages, but they don't show up in the conversation view until later. Sometimes even my own messages are lost for a while.

I noticed tracker-store and smartsearch are grinding the CPU while this happens. I tried 'kilall messaging-ui' as suggested upthread, and that seems to help concerning past messages, but newly incoming messages are again delayed.

Does anybody have a recommendation on how to fix this more prominently, short of "wipe your messaging db"?