Yeah, I recall a thread about a similar sort of thing about a year (maybe less) ago. Can't remember what it was called or what the solution, if any, was though.
Beep, does the odd looking audio actually sound OK? I'm just wondering if it's a bug in Sonar's wave graphic drawing algorithm or something. I tracked a (hardware) synth line the other day and it looked fine as I recorded it, then when Sonar did that kind of rescan over it and refreshed the graphic it became just a straight line that looked like silence though the audio played back OK, meters responded OK, just the image was wrong.
Deleting the contents of the picture cache to force Sonar to recreate the images restored normality - have you tried that?