Try changing the AutoMotion Plus settings or select 3D Optimize (as found on P.22 of the manual) or in the 3D menu (Press Tools on the Blu-Ray remote while it's playing) if that's possible.
If it's happening on the same place in the disc on two different players, it may be the transfer, or the specific scene.
I recently purchased a UN55C9000 in a bundle package, along with a Samsung BD-5900 Blu-Ray player. When I first hooked it up, we watched an IMAX promo disc in 3D, and it looked perfect. I watched the same video with a friend a couple of nights ago, and it looked like there was significant crosstalk issues in some scenes. I was able to pause it on a particularly notable scene, and could see the double image in my right eye when I closed my left eye.
I don't believe it's a problem with the Blu-Ray player, because the same issue is prevalent in my Playstation 3 when I viewed the same scene on that. Samsung support suggested I reset both the Blu-Ray player and the TV to factory settings, which I did - it didn't seem to help - if anything it made it more noticable.
I'm pretty much at a loss of what to do here - has anyone else run into this? And if anyone knows a way or setting to fix it it'd be greatly appreciated - I want to exchange it only as a last resort. Thanks in advance!