Sounds like the difference between the project being recorded at 48Khz sampling, saved. Then, the default sample rate for Sonar is later set to 44.1Khz. After that, reopening the CWP project, but somehow, Sonar keeps it in the new default sample-rate.
In preferences, under (Advanced) Clock, you may check to see that the Clock source is set to
Audio.
Otherwise, I don't know why a simple restart fixes the issue. That's a little weird.