Generally, each Effect Button can hold up to for assignments e.g. Effect Button II could toggle A, B, DLY and REV all together.
The LED only shows the first assignment. If you assigned B first adn there is a Distortion effect, the LED shows red regardless of the other assigned effect types.
If you now empty module B, the assignment is still there, but there is no effect and no color.
I guess, that is what happened in your case.
I suggest, you clear all the assignments and start from scratch. We might publish a Rig Manager supporting those assigments for the Player soon.