Here is how to reproduce/fix the problem.
I have tested this in SD only.
In the Kona Control Panel, set the video reference sync to Ref In, set the Control to Macintosh Desktop, and set the audio in for AES or SDI.
Select the clip(s) to capture and go into Batch Capture. Before the capture begins the desktop will appear on the KONA video. (This is not what I would expect as the proper behavior.) When the in point of the clip occurs the KONA video switches to the incomming video signal. The sync does not have time to lock up the audio and the result is out of sync for the clip. SDI audio will only result in a 2 frame audio offset, AES audio will have the 2 frame offset and a 1.5 second audio drop out at the begining of the captured clip.
The work around is the set the KONA Control Panel video reference to Video In prior to Batch capture.
Fred