This is a guess: but are those clips you are rendering out part of much, much larger original files? For example, if you have an hour video, but only need 5 seconds. When you render, perhaps it has to render the entire file due to the source codec, or perhaps the destination one. Or it could simply be a limitation of Premiere. Like I said, I can't replicate this, but I'm not using the same files/codecs as you, which is why I suspect it may be something specific to those files.
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