I just upgraded to 1.0.0 Beta 5e, commented out all my colour settings and ran it and all the colours have reverted to light grey, as they were prior to raising this issue. So, unless it's coinicidental or something shows up later, it looks like it might be fixed.
I think it was a style from the documentation css overlapping with the game css. I started to see the issue on my computer, so I make the documentation css style more targeted, and it seemed to fix it on mine, so I assume this was the issue. I think then the autosave functionality was carrying forward the issue to the compiled game.
It's my best theory right now.