The way i'm understanding your description sound like se is in wrong state, perhaps someone clicked or injected the i/o?
Can't you right click on the i/o and reverse logic? If all is as you say and light rays and board are good and you see I/o changing state then I would check that.
When you unplug the eyes does the problem stay the same? Is it going into nudging? Need alittle more info, if those are the light sticks I'm thinking if they way about an 1/8th inch cable that can break very easy, and the small board they sent in a lot of those operators that the eyes plug into I have had to replace a few times.