Kansas does not tax federal pensions and your program does not recognize that!

The program works. Line A13 requires that you mark the exempt amount of benefits. The program will do that for you once it has the information. Please  follow these steps (screenshots below):

1. return to the federal section, 
2. go to income, 
3. select the 1099-R, 
4. go through the entry process 
5. be sure that you  select your state, mark Kansas 
6. select Federal retirement
7. select Qualified Plan
8. Select cashed it out
9. Select Yes, regular payments
10. Select start year
11. Answer federal box 2a question

When you go back to Kansas, you will see the exemption. Here are screenshots of my John and Jane Doe fake return.

Reference: 

KS instructions

Federal side:

State side: