It's possible that the original file specified an audio delay. If you're using the mkvmerge GUI, you can change the audio track's delay in the Format specific options tab. Positive values delay the audio track, negative values advance it (all in milliseconds). If you're using the command line, you need to use the
--sync arguments. See the mkvmerge documentation for details. The documentation also shows you how to scale the audio delay evenly though out the video (instead of a set constant delay).
To determine the audio delay you need, you can use Media Player Classic along with the +/- keys to determine the delay. Alternatively, you can try to use a media information tool to see what the delay was on the original file.