Having the same problem I think I've got a fix but I'll have to do some more testing first.

Alright I've figured it out you've got to save your mod list using the mod to save the colours and if that doesn't work set up and colour your mod list before quitting to the main menu it'll ask if you want to restart click no because it'll delete your coloured mods once it hits the main menu click back into the mod list and save your mod list using the mod then you should be able to restart without deleting your colours.

thanks