Black Border and bad quality on Fraps Recording?

Hey guys, I record Mine craft Youtube channels with Fraps. Just recently I tried making my minecraft screen smaller to make my PvP better. I really want to keep it this way. I record a video with Fraps but when I uploaded it on Youtube, it uploaded with bad quality (480p) and black borders. Help would be appreciated (:
P.S: When I put the raw file into virtualdub it has two screens one is frozen one isn't.

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