Box 12D in a W2 form records the elective deferral of a 401K plan. Only the employee portion is listed here. There is no record of the employer contribution on the form. The amount in box 1 will differ from boxes 3 and 5, because although your 401k contributions reduces your wages subject to federal tax withholding, it doesn't reduce the amount subject to Social Security and Medicare tax.
As far as not signing up with the company's 401k plan, but still seeing an amount in box 12D, the company may have automatically put you in their plan and it is up to the employee to proactively opt out.
