The problem appears to be the call to htmlize inside genrow. If the data is inline, then wikilinks get expanded before they get here, and are OK. If the data is from an external file, the wikilinks aren't expanded, and htmlize will expand \[[single\_track\_lines]] into \[[single<em>track</em>lines]].
Oh, wait, I see the problem. IkiWiki::linkify is only called if the external file doesn't exist. If I remove this check and always call IkiWiki::linkify, then the problem is solved.
(this is inside /usr/share/perl5/IkiWiki/Plugin/table.pm).
I am rather confused what this check does, and the fact the comments are very different for CSV and DSV when the code is the same doesn't seem to help.