Deductions & credits

Does the employer's after-tax contribution belong in box 12 on the W2? I'm worried there will be a problem if the 5498-SA sent by the bank to the IRS after the tax due date will say $1700 and box12 will say $1200. Shouldn't the amounts be the same? Also instructions for Form 8889 say that the amount on line 9 should be the amount in box12. Again, will a discrepancy be a problem for the IRS? Thank you for your quick reply above.