Yes, what you have read is correct, anything you have withheld from your pay and put into your Company Sponsored 401(k) is tax-deferred, meaning, it won't be taxed until it is withdrawn.
I think what happened is you chose the wrong code from the drop-down menu for Box 12 of the Form W-2 input screen. Be sure you are selecting Code "D, Elective Deferrals to 401(k)". I played around with the W-2 Input screen and I think you may have selected Code "K, 20% Excise Tax- Golden Parachute".