When you put on a capo you change the tension needed to hold down the strings. So when you play a scale using some of the new 'pretend open strings' it will be wrong and you'll need to tweak a string here or there.

Also The Equally Tempered scale on a guitar will make things sound wrong in the new position.

You say you like the sound of the guitar better when using the capo. Perhaps you might want to play around with some different instruments, Say Tenor Guitar, or Bouzouki, or parlour guitar or even a half size student guitar.

And I'd go with what PoppaGator said. "Trust your ear"