OK, that is very strange. I wouldn't expect there to be any pops if you are writing the recorded buffers directly to disk unless your computer is struggling so much it can't keep up at all. Do you write directly to WAV file or are you processing in any way? You can increase the size and number of record buffers that might take a bit of the strain off your machine.
You can set the BufferMilliseconds property to 200 or 300 on WaveIn (or WaveInEvent which does use a background thread). Could also try increasing NumberOfBuffers from 2 to 3.
Mark