Hm, I had the same problem when I had an outside shop install a new clutch and flywheel, the jerks at the shop broke one of the speed sensor harnesses and all three lights came on.
I took it in to my dealer and innocently said I don't know what happened. They found it was one of the speed sensors had broken (as I knew) and replaced it for me under warranty.
Just be sure you are at a cool dealer. The first dealer I went to told me it was going to cost x hours or labor plus x dollars for parts so I left. The second dealer said if its a speed sensor, they will do it under warranty because they aren't supposed to just break but they do. It's kind of a known issue.
2006 Code Red Altima SE-R
- Injen CAI (now converted to WAI), AT Grounding Kit, AT S5 Front Grill, Debadged all but "SE R", Axxtion Short Throw Shifter, JWT Stage I Clutch & Lightweight Flywheel