The first thing that comes to mind from the description is that the combined signal might be peaking on playback even though neither signal individually does. Does it only happen during the loudest portions of the tracks? If you have two tracks with the exact same signal (and set to the exact same playback volume), the combined signal level will be a whopping 6dB louder (twice as loud) as just one track by itself. If the two signals are different, the increase will be somewhere from 3dB to 6db, depending on the sources. Try turning both tracks down on playback and see if it goes away.
There's so many thing that can cause pops and clicks, though. How frequently does it happen (every few seconds, constantly, once or twice in the recording)? Do the clicks and pops coincide with the loud parts of the material (i.e., are you just peaking)? Is your AC/refrigerator/something else kicking on and sending a spike through your system while you're recording? Bad channel on a pre-amp, mixer, soundcard? Lots of things to check.