If you export just audio do the pops go with it? Have you done a mixdown? Dose it always pop in the exact same spot? It could be a cumulative effect of playing the 44.1 and 48 together. Have you ramped up and down on ALL the sound clips on all your audio tracks? DV has a tendance to pop when a file is not faded down, even if there is no sound.
Hope this helps-
Matthew
Dual 500 G4
OSX 10.3.5
Ram 1.38
FCP 4.5/AE 6.5/DVDSP3