I solved the problem which was caused by the “Audio Input Present” checkbox being checked on the HD-Connect SI controller.
Quote from John from Convergent Design :
“The issue you are likely having deals with the audio in the HDV stream. The HD-Connect SI is setup to look for silent audio in order to fix an issue with JVC equipment. The result is that if a tape has silent audio, the video will blink.
To turn this off, install the controller application for the HD-Connect SI available on our website on the HD-Connect SI page. Connect your SI to your computer via 1394 and start the controller application. Click open and then uncheck Audio Input Present. This should fix your blinking video issue.”
Joel