"the IRS may not have gotten a copy of the W-2 from the employer"
This seems the most likely cause, either that or the Form W-2 filed with the IRS by the employer has information that differs from the W-2 information entered into TurboTax. In addition to providing the IRS with the information requested, make sure that all information from the W-2, particularly the employer name and EIN, were entered correctly into TurboTax's W-2 form.
