as you have found out, the two are not 100% compatible with each other.
they both look similar, but campagnolo uses ISO and shimano uses JIS which results in what you're seeing there.
You should look for an ISO square taper BB for centaur and below. Chorus and Record square taper uses yet another standard and will result in further complications.
I would check the sheldon BB spindle length database to see what you need.