First, those USB drives are garbage quality; check out these read/write tests submitted by users, looks like the average write speed is around 8MB/s. Get a better quality drive and it will be well worth the cost.
Second, it sounds like you're making a mistake in the export process -- are you moving things around somehow? That might be causing the secondary export and thus taking more time. It should only ever have to export the file(s) once, and then add new files the next time.