You're better off using the free Expression Encoder 3, which has a nice GUI and .NET object model exposing the important parameters, and is also faster and higher quality in general (basically all the Win7 perf improvements on XP and Vista, plus the quality improvements from the VC-1 Encoder SDK).
Windows Media Encoder is, what eight years old now, and has really lousy preprocessing in comparison.
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Ben Waggoner
Principal Video Specialist, Amazon Prime Video
My Compression Book
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