Hi Manuel,
Sorry for the 2 year delay in reply. Perhaps my reply will help someone else. I had the same problem with gray fonts instead of black fonts.
I solved this problem as follows:
Copy the LyX CSS file to your home directory:
cp $(locate lyx.css) ~/lyx.css
Add a CSS rule to your new lyx.css file:
.Mathjax { color: black; }
Read the source code for elyxer here:
http://nongnu.askapache.com//elyxer/elyxer-lyx-C.pyNotice that there exist options "--css" and "--embedcss".
Open LyX > Tools > Preferences > File Handling > Converters > "LyX -> HTML"
Change the "Converter:" line.
Before:
elyxer.py --mathjax remote --directory $$r $$i $$o
After: (I had no success with "~" or "$HOME", so I specify the actual path.)
elyxer.py --embedcss /home/kamil/lyx.css --mathjax remote --directory $$r $$i $$o