I’ve been emailing Blackmagic Design support (been working with Sarah who’s been very nice so far) for a similar issue with my Shuttle Thunderbolt.
I wanted to record gameplay from my Xbox 360 in 720p via HDMI with Media Express. On both of my tv’s, with both of my Xbox’s the output to the TV flickers. One of them seems to effect captured video like you showed, and one seems to just effect the output to the TV. But even that makes it really hard to play an action game when your screen cuts out for 1-3 seconds at a time.
I’ve tried combinations of all HDMI, all Component, and mixing the two types of cables and nothing seems to fix it. The product page even features “Record your Game Play!” and shows an Xbox controller, so I imagine it’s got to work somehow.
I’m hoping a solution presents itself soon.