Is it possible this has something to do with cancelling the AutoScan on startup mid-stream?
I had a case where I launched Sonar without my interface on. As soon as I realized it <got the message box telling me so> I switched it on, but as we all know, it's too late then. So as the scanner ramps up to scan my plugs, I kill Sonar to re-launch.
After relaunching, it did not re-scan and plugs as simple as Channel Tools showed up missing in the project.
After a restart of the PC, the scan kicked off and ran to the end smoothly. This fixed things for me.
Noel asks why you wouldn't have scan on startup enabled, and this is why for me. It's not worth the trouble if it can force you to restart your PC.