When I used iPhoneInterface I always exited iPhoneInterface, then restarted the phone. I've noticed in the past that if you leave iPhoneInterface on and restart the phone and try to type in more commands, it will give an error. I found that out a while back when I first started modding.
I agree. It's the best way to avoid any problems. Just wondering, have you tried the Manzana drag and drop program for modding? It's a lot easier than iPhoneInterface. I'm using that now and it makes a modding a lot quicker.
I actually enjoy the interface. I am a programmar and I feel more at home using the command prompt. The idea of using a UI to mod my phone kinda scared me just because of the whole bricking thing. I feel safer with the prompt but I know when I decide to change all my icons I may use it.