Originally Posted by Freebase Dali

The pops may not be caused by a peak in the recording itself, but a hard transition from having no sound, to having sound (even if it's just background noise). Although it's weird that you don't hear that until export.
If that's the case, the simple fix is, prior to exporting, to create a volume envelope that quickly ramps up from no sound, up to normal level. Obviously, you'll want a little lead time to do this in, but you wouldn't need more than a second of time for it to be effective.