I had a very similar experience the first time I had my headliner replaced for stains as well. Dome light wouldn't turn off. The overhead console didn't even have a sunroof switch. The ambient light and dome light switch weren't working right and it was all sorts of haywire. They eventually got it on the third try. Good luck!
2012 FF Ti HB Kona Blue, DCT, Built 5/24/2011, 401A + Ti Handling Package, Parking Technology Package, Winter Package, Moonroof, and MFT w/NAV at v3.8 129k miles and counting...