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While you are working on stabilizing a shot, you will be re-fetching frames from the source imagery fairly often, especially when you scrub through a shot to check the stabilization. If the source imagery is a QuickTime or AVI that does not have many (or any!) keyframes, random access into the shot will be slow, since the codec will have to decompress all the frames from the last keyframe to get to the one that is needed. This can require repeatedly decompressing the entire shot. It is not a SynthEyes problem, or even specific to stabilizing, but is a problem with the choice of codec settings.
If this happens (and it is not uncommon), you should save the movie as an image sequence (with no stabilization), and Shot/Change Shot Images to that version instead.
Alternatively, you may be able to assess the situation using the Padded display, turning the update mode to Neither, then scrubbing through the shot.
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