Flashing CEL indicates a "type A" misfire. Hook a scan tool up to it and pull the DTC's. Should be a P030x, where x could be 1-8 indicating what cylinders are misfiring. I would deffinetly NOT install any aftermarker tunes or other accessories in it until the dealer has this figured out. You don't want to give them any reason to void the warranty. IMO, it is probably a COP that is bad.