What code is in box 7 on your 1099-R?
Do you have non-deductible contributions in the IRA that were reported on a 8606 form?
How do you know it's not charging you tax? Or are you asking about the 10% Early Withdrawal Penalty? Do you have an amount in 1040 line 4b? Does it say Rollover by it or something? Try deleting the 1099R and re enter it.
Before filing, you can preview the 1040 or print the whole return