Sounds like what you are seeing is the missing 540 (even) lines from one eye being overlayed on top of the odd lines, and vice versa for the other eye. This is what LG does to claim that all 1080 lines are shown to each eye.
http://www.hometheater.com/content/closer-look-active-vs-passive-3d-flat-panelsQuote:
LG claims that its FPR panels are actually displaying all 1080 lines of information for each eye, but not at the same time. In the first 120th of a second, the odd lines of the left image are displayed in the odd lines on the screen and the odd lines of the right image are displayed in the even lines on the screen. Then, in the next 120th of a second, the even lines of the left image are displayed in the odd lines on the screen and the even lines of the right image are displayed in the even lines on the screen. (For more on this, see my discussion here.) This is very similar to interlacing, which has its own problems.
However, this puts some lines in the wrong place—even lines from the image in odd lines on the screen and vice versa—which would cause a slight but noticeable vertical judder. And even though all 1080 lines of information for each eye are being displayed, each eye sees only 540 lines of resolution at any given instant. Not only that, objects behind or in front of the screen plane will exhibit interlace artifacts.
Edited by Augerhandle - 7/30/12 at 3:20pm