I have a video in mkv format that shows two identical separate videos together, and not one over the other in vlc. On windows, I am able to play it adjusting deep, 3d mode (red cyan, with 3d TV and its glasses thorugh hdmi), etc. Bino does not work at all. I can only select rec cyan and it crashes on full screen. I am using ubuntu 11.10 with fully 3d support.
Normally an anaglyph (3D via red/blue glasses) video has to be a single file containing both color filters. You could use a video editor (there are many open source video editors available for Linux) to combine your two video files and export to a single anaglyph video file.