1099-R

Why am I being taxed on the difference between the gross distribution (box 1) and the taxable amount (box 2a)? The difference between those two is showing as income on my 1040. I did not receive the gross distribution amount. I received a check for the taxable amount and deposited it into my new account.

The reason there is a difference is because I closed one retirement account (annuity) and moved the funds to a new company on advice of my agent. There was a penalty for doing so.