This is a random issue and does not happen with all joined files.
When I join multiple VOBs using either Vobedit or copy /b command and then I try to encode them using StreamPro from Digital Rapids the final encoded WMV file sometimes doesn't contain the entire clip. It seems to cut off at the point a VOB would have been joined to another.
The merged VOB plays fine so I know the join is working.
Any ideas?
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