After a very long time, today I planned to watch Avatar 3D again and I discovered that the latest firmware update has fixed the flickering thing while watching 3D. Last time when I watched a 3D movie, I had to set Motionflow to Smooth to enjoy flicker free 3D. But now I can enjoy 3D without messing Motionflow. By the way I'm using the Sony TDG-BR250 3D glasses.
Sony XBR55HX929 / LG OLED55C6P
Denon x4000 / PS3 Slim / BDP-S6200
Roku 3 / WD TV Live /Chromecast / Fire TV stick
Speakers - DT PM1000 / PC2000 / Yamaha YSP-1600
Sub - Power Sound Audio S1500