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[p41]

Probably not the same problem but here is a similar situation
http://wdtvforum.com/main/index.php?topic=4450.0

[amature HD guy]

Did you encode the file yourself or download it.     The ref frames look ok but it could easily be a bad encode. 

I do not have these problems with ANY properly encoded 1080p MKVs.

I have the same movie stutter issue problem with 1080p files.  Sometimes also with 720p but much more consistently with 1080p files.
This may seem like a dumb question but how do you encode your own files?  Can I download an MKV file that someone has posted and then encode it to make sure that my WDTV will play it properly?