First, test your equipment. Set it up in front of your stereo and record some music. And listen. Then play around with your connections while recording. And listen. If it is still going on, switch out cables and record. And listen. Switch out the SD Card and record. And listen. Keep doing this until you've isolated the problem.
I think it might be as simple as a bad connector. This has happened to me a couple of times now, and I routinely tape down EVERYTHING. So Mike to the preamp--taped. RCAs out to the recorder--taped. Line in to the record--you guessed it, taped. On Off switch--yep, taped. It makes rigging up in the bathroom a little wierd, with the sound of gaffers tape, but fuck them--I just tell them its my "Depends" adult diapers.
To zap the offending pop, isolate it very close up on your wave editor, so the pop takes up half the screen. The turn the + into a 0, e.g., mute the offending section. If it is long, swap the other channel, so for the mili-second, it is mono.