Why are my employer's HSA contributions being taxed?

Box 12 with code W should include both employer direct contributions and any contributions you make via payroll deduction.   The program will add them back to your taxable income until you certify that you had qualifying HDHP insurance.  This step should come in the W-2 interview if you run all the steps, and it can also be accessed in the HSA interview on the Deductions and Credits page.  Make sure you answer all the questions and don't skip around.  Once you certify that you did have a qualifying health plan (and which months), the contributions will be taken back out of your taxable income.