I have a Canon 5D Mark III and I have noted that the last 4 frames of all my video clips have no audio (audio level is zero). This is independent of resolution, compression and framerate (ALL-I/IPB, 25/50 fps, 720p/1080i). I took my camera to the Canon Service Center. They replied that all Canon dslr's are working this way and that this is not an error but instead more of just the way they work. I'm not satisfied with that answer. What makes me concerned is that when scanning the internet it does not seem like anybody else have experienced this problem.
The problem can be seen with all my available video software i.e Final Cut Pro X, Premiere CS6, Quicktime, VLC ...
Have anybody else experienced this?

Perhaps the issue is that your camera records an extra 4 frames of video with each scene, and the audio stops where it is supposed to be. ;-) I know I am being funny, but the end of a scene is so fluid anyways, why not just record an extra half-second and be done with it?

My Panasonic gh3 doesn't record audio the first 8 frames of every recording which has been reported by other users, as long as your camera works otherwise I wouldn't worry about it. Those few missing audioframes won't make any difference.

It could be the NLE or playback software. It might not deal with the final packets of audio properly.

Have you tried playback with other decoders or different machines? (Sometimes faulty resources on a machine are shared by multiple apps.)