LaTeX.org

Thank you. Replacing eqnarray with align fixed the colour problem.

I apologise for not noticing cgneider's post. Here's the LaTeX output of a minimal example:

%% LyX 2.1.3 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[british]{report}
\usepackage[T1]{fontenc}
\usepackage[latin9 ...

Perhaps my automatic/by-hand description was misleading. The numbers still automatically update as things change, track equation labels that I add etc. It's just that right-click --> add equation number results in black text, whereas 1-line equations that are automatically numbered due to preamble ...

I'm writing my thesis in LyX. I frequently use long greyedout notes that contain display-line equations.* One-line equations in my thesis automatically number themselves, but some multi-line equation environments are necessary, because of multiple related equations or equations too long for one line ...