This can be caused by many different things including: bad audio connections, bad audio cables, broken sound cards, improper sample rates and more.
If you have bad audio, double check all the connections and hardware leading to the encoder PC.
If you can confirm that the audio sounds good all the way until it reaches the encoder PC, then proceed to check the sound card drivers, the sound card stability, and the sample rate. The sample rate needs to be locked at 44100. If the issue persists, contact us at streamsupport@amperwave.com.