Pensions are not taxable in the state of Florida however box 2a shows the full amount as taxable? after entering the amount my refund went down quite a bit

Florida has no state income tax so your retirement income is not being taxed by Florida.  But your retirement income can be taxable on your federal tax return.

Not sure what you are looking at.   Pension income is shown on lines 5a and 5b of your Form 1040.

The form is a 1099R  so the boxes you mentioned are empty

So you meant the box on the 1099R says the pension is taxable?   Yes---just enter the 1099R exactly the way it appears.   Again---depending on how much income you got from the pension---it might or might not be taxable on your federal return.  We cannot see your other income.