My payment was input correctly in the extension payments section and the payment still did not show up on line 32 of the 541. After talking to tech support, to solve the issue we found that my payment screen did not have the option to allocate from US or to specific state. To solve this problem:

In client information screen check Multi-state return and select the resident state.

In the state extension payment click on the + button to expand the payment and select the state as the source payment.

The payment should now show up on the return.

I hope this helps with anyone else that has this same problem. Tech support said this was a first for him.