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What version of AE do you use and which OS? There are some conditions where the PNG-CoDec used in the clips will cause iisues in older versions of AE, both on Wiundows and Mac. Have you tried converting the clips in QT Pro, say to the animation CoDec?
I'm using After Effects cs3 (22.214.171.124) on a mac.. The problem is unpredictable.. it only happens sometimes.. and never in a consistent way. I suppose I'll try converting the clips in QT, but there are lots of them, so that will take a while, but if I have no choice then I'll do that.
Do you know if there is a fix, or update that corrects this problem?
Well, those things will have to be fixed in Quicktime itself, if they are known to the mighty Apple... The only thing you could try is to disable or modify the settings for hardware acceleration and legacy CoDec usage, perhaps that can resolve your immediate problems without extra conversions.