"I know about the On2 VP6 batch limitation per day and month"
That's only a limitation applied by Sorenson, no other Mac encoding application, eg Episode, does this...
That said - it souds like Squeeze it getting hung-up with one of your jobs and that is stalling your process. - Considering the huge number of files you need to process, I'd be looking at a far more enterprise level solution to do the job. Squeeze is quite obviously a (buggy*) desktop only product.
* Use search to see how many other have problems with it
+
http://forums.creativecow.net/readpost/117/856907
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Please post back saying what solved your problem. It could help others, and saying 'thanks' is free!
