CMake configuration isn't applied from Kit Manager

Reproduction steps:

1. Go to Project Tab
2. Press the "Manage Kits..." button
3. Press to your current kit
4. Press "change" CMake Configuration
5. Add variables e.g. (ABC=1)
6. Apply changes
7. Wait for reconfiguration

Misbehavior:

      ABC variable is not in CMake variables list

Expected behavior:

     ABC is presented in the list

If try to delete a variable it will be in the list but it shouldn't be.