My Samsung LN46C650 behaves the same way. I got it from Amazon in May 2010. It started out occasionally flickering when using the Roku (streaming Netflix). Then it got more frequent and started happening on cable channels, DVD, DVR. Usually the first 15 minutes or so would be fine and then it would start for no apparent reason. If I could stand watching it for very long, it would occasionally stop flickering for a few minutes and then start again. Damned annoying. & After a while it makes you motion sick to watch the TV.
I saw all the posts about cutting Jumper JP852 but was worried about doing surgery on my TV without really knowing what function I was disabling. I contacted Samsung through their chat line and asked them what JP852 did & what I might be disabling if I cut it. I could not get a straight answer out of the guy - not even a definitive "Don't do that because it will cause feature XYZ to no longer function".
He did recommend that I disconnect all the devices (DVR, Roku, etc) and then use the TV's self diagnostic "Picture Test" feature to see if it still flickered. Here's a link he sent me explaining how to do the Picture test:
http://support-us.samsung.com/cyber/popup/iframe/pop_troubleshooting_fr.jsp?idx=350987&modelname=LN46C650L1F&modelcode=LN46C650L1FXZA&session_id=&from_osc=&__ncforminfo=Q8I2TFGuMYpU6ZnVBTul4pVDdIK81ST3FgGIOAgCt8ONN9JVF5PUCLivmLPXUXzlYWzKkh8XFMLBxb1MxZbEs3ZjwLowL2Xriqr49YmcHKY%3D
SO I disconnected everything and did the test, and - SURPRISE! - the TV flickered as soon as the static test image appeared on the screen. Keep in mind that this is a static image built into the TV's memory. To me, that seems like pretty clear evidence that it is NOT a broken DVR or a bad cable connection - Its the TV itself. So if you are worried like me, I'd suggest trying that 5 minute test before you make a decision to cut the jumper.
I finally got up the nerve to cut the Jumper today, after checking on the price of replacement Power boards - about $100 each. So I figured, I know its the TV and the damage will be limited to a hundred bucks or so if this doesn't work. When I opened up the case, I found that it looks just like the pictures in this really good repair post:
http://www.instructables.com/id/How-to-fix-Samsung-LN46C630-screen-flickering-issu/
As expected, I have board BN44-00341B and Jumper JP852 was clearly labelled and right where it was supposed to be. I gave the capacitors a quick visual check just to be sure they were o.k. & they were all fine. And I took care to not touch anything on the "HOT" side of the board so I didn't fry any components nor get an ugly capacitor-shock.
I snipped that jumper wire in the center, bent the top and bottom halves about 45-degrees away from each other and closed it back up. And now the TV is working fine. No flicker when using any of the devices and No flicker on the built in Picture Test either!
Bottom line: I cannot tell that its not a brand new TV - the original picture quality is completely back. Thanks to all who have tried this in the past and posted the details for folks like me to see. As with several others, I will re-post if the performance changes or the flicker somehow comes back but I suspect I won't need to.