This just happened to me today, I did not restart or do a complete shut down on the unit before posting this.
Here's the problem that has arisen.
I clip my 1 channel audio track to where I want it, right click on it, choose apply time effects, set it to 110%, process it and now at the beginning of the clip there's a frame with a clicking sound that only shows up on the other channel that my audio is not on.
I guess a quick fix would be to pan the audio only to the channel I'm using, but I would like to cure the problem and not "band-aid" it because I do use alot of audio with it coming from both channels.
"Some people dream of worthy accomplishments, while others stay awake and do them."