(v. 2.72) Input movie's audio/video is in sync, but VSE output is floating and desynchronized between audio and video I've captured some .mkv files with Simple Screen Recorder (SSR).
When I watch these individual files, they play fine in Mplayer. The sound and image are in perfect sync. I hear clicks from my mouse and they match with actions on the screen.

While editing (A/V Sync is on) in Blender's Video Sequence Editor (VSE) it all seems rather fine - I can not play it back smoothly from Blender (640x480@60FPS, h.264 losless, stereo FLAC audio), but it doesn't seem to float too much. Just a little, especially when I start in the middle of a clip.

I rendered the movie, and the sound is completely off with timing in relation to the motion picture. It's floating around by a couple of seconds (an event happens, a few seconds later I hear sounds that were related to the event I saw earliest etc.).

I tried re-rendering the movie after enabling and generating timecode (Free run mode) for all movie clips. It didn't help at all.

What is happening? Is this a bug? I'm having these sync issues for years now.
My guess would be that Blender is not decompressing the file successfully. Best solution is to transcode the source media (with non Blender app) to be Blender friendly but sadly this will probably increase file sizes a lot.