My audio often does not start at the beginning of a track and ends prior to where Sonar thinks the end of the song is. I solve this issue by, in track view, selecting only the audio to be exported. Like this:
CNTL-A to select all audio clips
Set From and Through points using the Selection toolbar
I ALWAYS set markers in my projects for beginning, end, verse1, chorus1, etc. which makes setting the from and through points a breeze, among other things...