If you were also using some files without audio this would cause them to play fast i would think? would one just slow the playback speed for that layer down to compensate or am I missing a better solution here.
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yes it would cause them to play fast-
if you are using just video files - you use one of the frame rates that is locked to the screen
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the 23.98 frame rate problem is a very specific problem - as it doesnt divide evenly into anything at all in vga/dvi world - and if you want to preserve the time length of the clip and not double up any frames -