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For flash encoding in particular, your bottle neck is likely CPU. I'd throw the fastest quadcore processor I could find at it.
Look at any other potential bottlenecks as well. I wouldn't encode across the LAN, i'd make it local with the files on hard drive on encoding machine. And the drive doing the work should be a fast one.
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Just did all that. My computer guy says that the next generation of video cards will solve my problem. But at the moment, I just have to be patiient and let it chug along.