Whenever a Rich Media Annotation is being handled, Acrobat/Reader must load the Flash Player extension, decompress the SWF/video data, and hand it across. As a 32-bit application that involves a bunch of processor-intensive juggling of resources so it's not uncommon to wait a second or two. There's a similar pause when the extension is deactivated. It depends on how large the assets are, if there's more than one running at the same time, etc. but there is no way to avoid it.
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