I think your accountant did not explain things to you properly.
Under IRS regulations, this type of benefit plan is handled according you to agreeing to a salary reduction, with the money being sent by the employer to the HSA plan on your behalf. Therefore, all contributions made by an employer plan (including your own money plus any match) are considered "employer" contributions by regulation and are included on your W-2 with code W. The contributions are already subtracted from your box 1 federal and box 16 state taxable wages. You already got the maximum benefit possible and aren't being taxed on the money. You can't take another tax deduction for the same money.
If you made extra contributions out of pocket (not through payroll) they are tax deductible, as long as your payroll plus out of pocket contributions are not more than the allowed maximum for your age and type of insurance.
If your box 16 state wages are higher than your box 1 federal wages, you may have a problem with your payroll department, but not with your tax return.
