As I said, I figured out the cause and fixed it, but I can't remember the exact details. It was just one of those things that Windows/PCs sometimes do where a setting gets altered by one thing and not reset by another. It stuck in my head because my first thought was that my then interface was shot, and it took me a while to track down the problem. I'm not sure I ever really got to the bottom of it because it never recurred but I couldn't reproduce it either. I uninstalled and reinstalled the audio driver, reset the relevant preferences in Sonar whether they needed it or not, rebooted and the problem never came back.

I'd previously installed a few media players and codecs, which I uninstalled at the same time and didn't reinstall. I suspect one of them had done something, but no conclusive evidence.

Sorry to be so vague, but it was a one-off years ago.

I should add that the project in question was a work in progress and already contained MIDI and audio from previous work. The glitch happened when I opened it the first time I tried to record a new track. For some reason playback of the existing tracks was OK.

I doubt you're having the same problem, though I would check that sample rate and clock source are set correctly in Sonar and stay that way, reinstall drivers etc.