Sorry - I fail to see the problem. 401(k) contributions are not in box 1.
You said above that box 3 agrees with your pay stub. And box 12 plus box 1 equal box 3, so box 1 plus box 12 would also equal the pay stub.
If you think it is wrong then ask your employer for an explanation. I can't see your pay stub or your W-2.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
