One more thing. We think it may be related to the workstation. One workstation can render out perfect, the other renders out the files with errors. Could it be that the after effects cs3 they are using, which are different versions be the problem. or quicktimes, which is also different versions, be the problem. The one that works has quicktimes 7.3 and the one that has the problems is quicktimes 7.4.
thanks, hope i havent confused you.