Mplayer is a software only solution that does not really make use of any of the hardware acceleration of the phone. This means it is rather slow to playback since it has to use the CPU solely for this purpose. It also depends on the bitrate of your file realistically, and it is too high, then audio will be decoded slower than the video. Mainly the HD ones that are 720p and above.

The only way to get past this is to do a conversion of the file from MKV to MP4 (a format that is accelerated from the native player) or you can try and overclock your CPU up to 900+ Mhz to see if that helps.