Well, couldn't find a way of stopping mencoder from overlying the 2 subtitles, but I found an easy workaround.
I added to my conversion script a new step at the start that checks if the original file's extension is mkv, and if so, removes any subtitles from it using this command:
mkvmerge -S -o original.mkv /tmp/no_subtitles.mkv
then I use the output of this command instead of my "original" file and there's no embedded subtitles to supress