This is just a guess, but maybe it’ll help.
On my C100, if you don’t force Adobe Premiere to interpret the footage as progressive, then you get aliasing artifacts that look a lot like this. Once you do an Interpret Footage in Premiere, it looks good.
Perhaps there’s a similar situation with the output of the HDSDI of the camera — that the Hyperdeck Shuttle is misinterpreting it?
How does Premiere see the Hyperdeck footage — progressive or interlaced? If Interlaced, if you force it to be interpreted as Progressive, does that clean it up? Or, can you force the Hyperdeck shuttle to interpret the incoming signal as progressive?