@craigw a few questions to help narrow this
Is your capture interlaced or progressive?
Is your video (the files you play back) 59.94 or 60? and Interlaced or progressive?
Did you try out of curiosity the 29.97 setting?
Are you using the blackmagic capture driver or the windows one?
How many inputs are you running?
What are you general service tasks set to?
What are your outputs set to (screenshot the NVIDIA settings if you can)?
Just a quick troubleshoot to identify the problem, With no inputs enabled at all do you get the glitch?
Can you switch your capture to 60fps (I know you will not get an image from your inputs) and see if you get the glitch?