I assume this is rather related to overlay and the way it's handeled. So, first thing, I assume you are using "EVR" as rendering methode (BSPLayer select it as default). So, please try changin this to any other methode )(rightclick -> options -> preferences -> vide -> video rendering". I suggest to try first VMR9 renderless and after internal renderer default.
Second, as BSPeter asked in the post above, please state here the exact codecs used to play the files.
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