For a backdoor to work it must be a non-deductible Traditional IRA contribution - you do not want not to be deducted.
It sounds like you might be entering both the $6,000 2019 contribution and the $5,500 2018 contribution made in 2019 in the 2019 interview. Only the $6,000 can be entered. The $5,500 2018 contribution can only be reported on your 2018 tax return and if for a backdoor Roth, must also be non-deductible and reported on a 2018 8606 form that is part of your 2018 tax return.
When entering the 1099-R for the conversion only the 2019 $6,000 contribution will be on the 2019 8606 line 1, the 2018 $5,500 contribution you enter when the 1099-R interview asks for prior year non-deductible contributions and you enter the 2018 8606 line 14 amount (which should be the $5,500) and that will go on the 2018 8606 line 2 so that the total $11,500 will be on line 3.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
