Well I located the problem.
It was a clip that didn't have any audio data in it. That must have been the "padded with silence" part of the error message.
When I looked at its properties, on the Audio Files tab, it showed that if consisted of two files:
ProjectName etc, Edit (2).wav
ProjectName etc, Mix (16).wav
Both of those files are in the audio folder and can be opened in a new Sonar project and play fine. But when referenced for this particular clip in the project they belong to, they cause Sonar to detect "a corrupt audio region."
I don't understand how can a clip can have two wave files associated with it? I always thought a clip was either an entire wave file or some a portion of a wave file... but always just one file.