Default Auto Staging is Broken

I like to make my own custom staging sequence instead of using the default sequence. Let's say I were to make a rocket, and configure my custom staging sequence, and then test-fly the rocket, and come back in the designer; the designer will change my staging sequence and mess it up. Even if I 'Save' my 'Craft', and then fly it, then come back in the designer; it'll still mess up my custom staging sequence.