Quoted from Pinballomatic:BAG board mounted under the playfield controls all of the lighting more or less. There is a mini USB connector on that board which can come loose or get misaligned in its socket. It's the only mini-USB under the field and usually has a factory tie-wrap on it to hold it in place. Examine and re-seat or straighten if needed. The other end of that USB cable plugs into the "bottom" of the motherboard below the metal box behind the monitor (with the security dongle and the VGA and everything else). Unseat and re-seat the USBs there with game power off. Don't move them to other ports, just unplug and replug.
This is an old post, but I wanted to thank you for it. I was having the same issue with my Wonka lighting all of a sudden. Reseating the USB seems to have fixed the issue.