Encoding issue in CS6

When I encode video to a WMV file (bitrate 1500/3000) in Adobe Encoder CS6, the first fifteen to thirty seconds of video appears muddy and then corrects itself. When looking at it on the Premiere timeline it looks fine throughout. Any ideas on what could cause this?

After it has been encoded, I've watched it on a Toshiba 32" monitor and also a 17" Dell. Playback on the PP timeline using the Toshiba is fine. The problem happens after it has been encoded.

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