That makes, since. The issue would be with that underlying custom logic. There must be a case transaction block that is conditionally included, or similar, based on the user inputs you are describing. Someone would need to dig into the custom case definitions and debug from there.
You would likely find the Web Apps Data Preview tool quite helpful, here, since it will show you the state of your form as you fill it out and it may help you understand what the custom logic is doing and how to fix it.