TomHelvey
The OP is saying that the pops happen when the transport is started and stopped regardless of what is recorded. It has nothing to do with clips or zero crossing. I get the same thing too even with only instrument tracks. I think it's an artifact of processing start and stop. I usually ignore it, it hasn't blown my speakers yet and it doesn't show up in the final mix.
Electrons charging and discharging

Check your audio drive thru.
If not your hardware DA/AD converters, the sound-card driver, the settings within Sonar (try altered values to test).
Those mischievous electrons hanging around the entrance and exit of Sonar need to be tamed