There is an issue in the current versions of Pro Tools 11 and 12 which can result in the length of the output audio created by VocALign being too long. The signal will be followed by an area of silence.
To avoid this issue you need to do the following:
VocALign Project Press the Align button before pressing Spot.
VocAlign Pro< - Press the Process button before pressing Spot.
We are working with Avid to fix this issue in later versions of Pro Tools.