I have been experiencing the same problem. A strange jackhammering audio glitch when crossfading from silence.
As a workaround until this problem is officially addressed, when I render out the audio separately as a wav, the soundtrack is rendered without glitches.
So for the past few days I have been rendering out my audio and video separately, syncing it back together in a new sequence and rendering it again from there.
This works if you are in a pinch, but this problem must be fixed.