As you unplug the boards and connectors, look for oxidation on the molex pins. These connectors can't seem to handle the power and/or vibrations over time and oxidize. A little cleaning with a fiberglass sanding pen and a very light coat of dielectric grease could solve it.
As Zitt said, the signal travels from board to board. Once the signal gets corrupted at a questionable connector, all down stream lights can be messed up.