For the past two years, I have maxed out my HSA via biweekly payroll deductions. These are listed on my paystubs as under "deductions" (along with taxes, parking, 401k, and health insurance). My employer does not contribute to my HSA at all. Deeply buried elsewhere on my HR website, it breaks the deductions out on a yearly basis and says the HSA, parking, 401k, and health insurance are pretax.
There is no box 12 code W on my W2. But, per the "Instructions for Employees", I think there should be, as it reads "W—Employer contributions (including amounts the employee elected to contribute using a section 125 (cafeteria) plan) to your health savings account. Report on Form 8889, Health Savings Accounts (HSAs)."
Last year, my accountant took a deduction for my HSA contributions, assuming they were post-tax because they did not appear on the W2 (his words). That seemed right at the time, but in retrospect, we obviously double-dipped, right? To make it more confusing, the total gross wages on my final paystub is about $5000 higher than what is reported in Box 1 of the W2. Is the HSA already pulled out? I can't get it to work out no matter how I add up the numbers.
Any help before I bring this up with HR would be appreciated. I know it's ultimately my fault, but I'm not happy about having to amend the prior tax return and I can't be the only employee this affects, right?