Using VirtualDub, I discover that in the output file, every 15 frames, two frames where identical (of course this is not the case in the original file), whatever the output compression format was (I was using "custom" to configure the output file). After a lot of trials / errors, I discovered that by configuring a project to be NTSC 29.97 and asking for the output video file to be "same as project settings", this was fixed.
I upgraded to VS11 recently and the problem is still here, but even worse this workaround does not work anymore.
It seems that VS11 is forcing some up/down scaling computing of frame rates and I don't understand why (again input frame rate == output frame rate). ANy help would be welcome
