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Alex, the issue you are seeing is because at a certain point, the system isn't polling the port fast enough to capture the video. Usually this happens over time as the longer you capture, the more ram gets used up, the less buffer you have to work with, and sooner or later the system is caught having to write out to disk and it doesn't look at the video port for a few frames. It can take a few more frames to resysnc and keep capturing.
This is often the case using built in Firewire ports. Better software will work better to reduce this problem, as they will better manage memory and such.
How fast is your PC?
Alex
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