Why am I being penalized for my 1099-R after tax annuity distribution? Box 1, Box 2a, and Box 2b are checked. Thanks in advance!

If your annuity distribution is non-taxable, ‌box 2a should be blank or have zeroes. It needs to be entered exactly the way it is.  If it's incorrect, you should contact your plan administrator and request a corrected Form 1099-R.

Thanks for the response.  According to Turbotax the 1099-R preparer enters the full amount of the distribution in Box 2a, but if they don't know the taxable basis they also check box 2b, leaving it up to the tax filer to determine the taxable amount. Unfortunately I could not find anywhere on Turbotax to do this.