I've just been struggling with my custom setting for `org-latex-to-html-convert-command` outputting many math snippets wrong. The fault was mine: I didn't correctly shell-quote the input. I propose to add a warning in the docstring, because many people will trip the same problem.
The thing is that double-quotes don't work in shell commands. I had \"%i\", but it should've been '%i': (setopt org-latex-to-html-convert-command "node /home/kept/pub/texToMathML.js \"%i\"") Math snippets that start with $, like $y = 200$ of course get butchered into just " = 200$" because of course the first $y gets interpreted as a shell environment variable.