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And how does the image look before crop/resize? It is easy to see if quality is lost there or if it was already bad before.
Look this for example:
The first is only resized without crop, the second is cropped and resized... the one cropped has lost a bit of quality: look very well in the low part of the image near the 640x490 and the KB, it is a bit blurred, but the one without crop isn't blurred in that place...
In MPC, can you also check what option is selected in View -> Options -> Output -> Direct Show Video ?
"System Default" also in Real media video, Quick time video and Directshow audio.