I've had this problem before, now I have it once again, even in AE CS4.
I have a movie clip converted with an MPEG codec.
In Windows Media Player it plays just fine, perfect, no glitches.
In AE - most of it plays fine, but it bugs at certain points, the current frame mixes with previous frames and everything gets blocky and darker. This is quite an issue, because after I export - the resulted movie still has those glitchy couple of frames at times.
Could this be a codec issue? A common one?
Since I'm dealing with it on a second computer and version of AE...
You don't have the latest version AE, which is AE 10 (aka CS5).
So the following still applies:
Dave's Stock Answer #1:
If the footage you imported into AE is any kind of the following -- footage in an HDV acquisition codec, MPEG1, MPEG2, AVCHD, mp4, mts, m2t, H.261 or H.264 -- you need to convert it to a different codec.
These kinds of footage use temporal, or interframe compression. They have keyframes at regular intervals, containing complete frame information. However, the frames in between do NOT have complete information. Interframe codecs toss out duplicated information.
In order to maintain peak rendering efficiency, AE needs complete information for each and every frame. But because these kinds of footage contain only partial information, AE freaks out, resulting in a wide variety of problems.
I'm a Mac guy, so I like to convert to Quicktime movies in the Animation or PNG codecs; both are lossless. I'll use Apple's Compressor, Adobe Media Encoder or Quicktime Pro to do it.
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