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Information reported in box 12 is generally for informational purposes only.
Employer HSA contributions must be reported in Box 12 of the W2 under code "W." This is for informational purposes only.
The $4,000 in contributions are not taxable income to you. See the discussion of HSAs in the W2 instructions. Look on page 5 on the right hand side - roughly middle of the page. Link is here: http://www.irs.gov/pub/irs-pdf/iw2w3.pdf
There is no deduction on line 25 of the 1040 since the employer made the contribution for you on your behalf tax-free.
Your distributions are not considered taxable income provided they were used for qualifying medical expenses.
Please let me know if you need clarification or have any further questions.