Videos with transitions have garbage when played back

I have recurring problems when inserting videos made with Keynote (6.5.3) and exported to QuickTime. Please see DropBox link for example video.
Image in video is 1500 x 1000 px, imported into Keynote in original size—no scaling.

Given the window size you cite, you are likely generating a very high bitrate video file and that could cause the symptoms you report. The iPad, where most *.ibooks files are played back, is 1024 X 768 so all of those "extra" pixels are not doing any good. Without access to the file, this is all conjecture. There are a lot of variables at work. Fortunately, iBA 2.2 now does a much better job of optimizing video than earlier versions of the optimizer did.. The optimizer does its best work when handed files with a reasonable bit rate. Share a link to that video file so we can scope it out and be more precise.

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