The issue also appears when resampling from 44100 to 48000Hz, but less often.
It can be best observed when resampling a constant signal. Lets say a file with shorts of value 16384. Then, every several thousand samples a 0 will be present in the output. (and ripples around it). If the value of FFTFIRLEN is decreased to 65536/8, then the 0s are more often in the output signal.