I run into this quite frequently too. I agree with the "hitting play" thing mentioned above. It does seem to work. Also, make sure you just let things settle a minute or so before saving. Like if you do any major editing or bouncing, etc. Sometimes I catch myself hitting save right after I make some sort of adjustment. I think Sonar is still processing the edit or whatever, and it can't handle saving at the same time.
I've also noticed I have this problem while closing a project. But if I wait a minute or two before closing (and hit play/stop), it seems to close ok. Fortunately when this happens during closing, I don't lose any work because I've saved prior.
I've also learned to let my computer sit for a couple minutes after booting before opening a project. Turn it on, go grab a beer or something, then come back 10 minutes later when the computer is fully booted and ready to go. Starting early always caused me problems.
~Jeff