Channel Vocoder producing output with "click" sounds
I think it could be one of two issues.

What is your frame overlap? if the frame overlap is something less than 40% or so you will begin to get undesired artefacts when you perform overlap add synthesis at the end. Try an overlap of 50-80% (although more computationally expensive, it provides greater frequency resolution). 

The second consideration which goes hand in hand with the above suggestion. Are you using any kind of analysis window on your framed signal? Perhaps try using a tapered window such has hamming, Blackmann or Hanning. This will help minimise spectral leakage between frames. Hope this helps.