If you put an H.264 stream into an mkv container there can be two locations in which aspect ratio information is stored:
1. within the H.264 bitstream
2. within the mkv header
Some players rely on 2 and some players rely on 1. The x264 paramter --sar will only write 1, mkvmerge will only write 2. You cannot use mkvmerge to patch 1.
There is a tool which can change 1 without re-encoding but it's neither trivial to use nor stable:
http://forum.doom9.org/showthread.php?t=152419