I agree with Nauli - the dealership most likely wouldn't have removed a flash tune. Is it a turbo back exhaust or just a muffler? Regardless, there is no way that an exhaust would be affecting idle but it may help in determining whether the car has been tuned. If it only has a diff-back exhaust, then the odds of the
ECU having been reflashed are very, very low.
Does it try to stall all the time (once warm) or is it random? The cold start settings are different so that will be why it runs fine when cold. Have you seen any check engine lights come up on the dash or has the light been flashing on your cruise control switch? How does it drive under boost??