Results in:
https://i.imgur.com/C3VREVD.png
Instead of: (Generated in pdflatex)
https://i.imgur.com/AvUTMA0.png
I think it has something to do with how tikz handles references. compiling this with texify.exe requires multiple passes.
Thanks for the report. Unfortunately this is probably related to the internals of TikZJax and I have neither the time nor the knowledge to solve it. No idea how I'd get it to run multiple passes.
Using this chemfig figure: