I just tested this with a Quadro P400/Roku and couldn’t reproduce, sorry. But, two notes:
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Try temporarily turning off hardware acceleration. The comment about VC-1 being a single-thread decode is somewhat irrelevant; you’re using hardware acceleration, so the software-decode CPU threading doesn’t normally matter for you. However, just as a test, try turning off the acceleration to see if the transcode works. You have plenty of CPU to handle a single-thread software transcode test. If it works with software encoding, at least we can check a few directions such as video drivers.
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The only device playing it properly (PMP) is using direct play. Heads up that the Shield does play VC-1 natively, but AFAIK that’s temporarily broken due to something nvidia did in the 8.0 update. That will hopefully be resolved soon, and Plex won’t need to transcode VC-1 for that device again anymore. There’s a hotfix available, you can read here to catch up. @Achilles do you know if the Shield still requires a hotfix for VC-1 playback?