Huh… For what it's worth it works fine on my Arch (my primary development system is actually Arch Linux); I just compiled it successfully.
Maybe run ldconfig, make sure that the libraries are actually present in /usr/lib and that the symlinks are correct. If in doubt paste the output of "ls -l /usr/lib/lib{magic,ebml,matroska}*" and attach config.log to your post.
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Latest MKVToolNix is v83.0
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