This can happen for a few reasons.
The first one is the most simple: Your new heatsink is not cooling the card effectively. This can result in picture distortion, or total loss eventually. This is the first thing that I would check, because if this is the problem, you could lose more than just a few pixels worth of data soon. If your card has a temperature sensor built-in, which many of them do nowadays, monitor that, and see what temps it is maintaining. (You may need an outside program, such as MotherBoardMonitor to read the sensor.)
The second one may involve the heatsink grease compound that should be between the heatsink and the chips. If some of that compound somehow got onto the metal part that connects the card to the computer, you may be getting a bad connection between the two. If that is the case, you can clean it with alcohol, Prepsol, or some other 'ol.
Third may be that the card is simply not seated into the slot very well. Try pulling the card out and putting it back in to see if that helps. Also make sure that if it uses a direct power cable, (which I think that one does,) that it is seated completely.
I have not had a whole lot of luck with the new fanless cards, they never seem to keep things as cool as they claim, but I tend to put my equipment through the paces fairly hard most of the time. It sounds to me that you just may be experiencing some straight-up heat issues - which would explain why you are only having it during the heating times of the computer, (start-up, games, etc.)