I have encountered this when selecting Cinema mode instead of Standard mode on older Panasonic plasmas such as TH-46PZ80B. In particular, the scene in "Contact" in young Ellie's bedroom, the walls with the subtle patterning strobe quite badly; I have a feeling this is a visual artefact of the dithering that our eyes are particularly sensitive to. I notice that the effect is considerably reduced on the Normal preset, but as a result, the panel dithers more (Cinema seems to drop the field rate and give it more bit depth per field.)
It is very unlikely to be the video card. A video card deals with digital signals almost entirely nowadays, presuming you are using HDMI, DVI or DisplayPort, and it cannot cause the effect you complain about.