I have never experienced a glitch in the game (I have played it more than once) and offhand I don't know anyone else who has either, so a glitch seems doubtful.
What I am wondering is if there is some little thing that you haven't done in the game prior to this, that perhaps the game doesn't recognize that the colors are correct until you have done it.
Ah, check this out - this is from a discussion on the HeR Interactive forum:
Windmill color blocks Maybe that's where the trouble lies?