Try disabling the 64-bit double-precision engine. I reported an issue some time ago about getting meter-pegging pops from with an auto-stretched section of silent audio. I only ever saw it in one project, but that project still does it in Platinum unless I disable the 64-bit double-precision engine, but it stops with the transport.
If you're still hearing noise when SONAR's audio engine is off, it would seem that something's going on with your interface driver or some other app sharing the driver.