I have sorted this annoyance on my LG DM2350D 3D TV. The fix may work for other LG TV owners experiencing the same issue.
I was having brightness fluctuation problems with my LG DM2350D whenever I watched Blu-ray 3Ds. It was really annoying but not enough to return the TV as I'd already had to send a previous one back a few weeks ago. I have finally got rid of this annoying phenomenon though by switching to either the "Expert1" or "Expert2" preset. Both of these Picture presets have a Day/Night logo ("ISF") next to them. None of the other presets like "standard" or "vivid" have this logo. Now the picture with the "Expert" presets is noticeably darker than the other ones but at least there are no brightness fluctuations. I can handle that for Blu-ray 3D and switch back to "Vivid" when watching 3D over USB or via the PC (I've yet to see these brightness fluctuations in these modes).
Addition...while in RGB or HDMI (with no disc inserted) you can go into picture settings and make adjustments to the "Expert" presets to suit your tastes. I've managed to get it looking as bright and clear as the "vivid" preset but without the brightness fluctuations. I'm very happy now.