I'm having the same issue on a machine unboxed yesterday, with about three hours of play. Machine #477.
All of the controlled lamps that are connected to or branch off of board 3 (3, 3A, 3B, 3C, etc) which includes the GI, go out randomly. They may flicker off then back on, or stay off. The lamps that are on board 8 and it's children remain functional. If I disconnect the cable that runs between the CPU and board 3, the GI comes back on. If I plug it back in, the lamps go out again after about a second when the CPU board starts controlling the lamps again.
This can happen during gameplay, or even when in service menu.
I phoned Stern this morning and got the same response. It's an identified software issue, which should be resolved in the next code release. I seem to recall they said it should be released within the next day or two.