PC
We have the exact same configuration, except we installed OS 10.3.9 not the dual 2.7, and we have a different Raid.
We have no sync issues if we set the KONA Control Panel to sync on Video In before we begin the batch capture.
If the KONA Control Panel is set to sync on Ref In or FreeRun then you will get a 2 -4 frame audio sync offset as well as an audio pop at the head of each clip of the Batch Capture.
Fred