You didn't say anything about the audio format. H264 is the video compression format and mkv is the container format.
I'd guess that the audio format in your other video files is different than in the mkv files. For instance, if the mkv files contain audio in 5.1 AC3 format you may need to adjust the channel mixer settings in FFDShow audio decoder's options.
Also, the "volume > normalise" feature might help. Enable it and try amplification values up to 500% or so.
or can you put this up to say 200% without any undesired effects?
In general, there is no reason to be afraid of any adjustment that produces the desired result unless the output sounds distorded. Besides that it does not sound good your tweeters might be in danger because the clipped signal contains uncontrolled distortion components that may be louder than the tweeters are designed to handle.