transpose unreliable

I am getting some strange effects withe the transpose tool. It doesnt sometime do what you expect - like transpose to a key you asked for it ends up with something else. Are there limitations it its use - like you can only do the operation once on the original score

I have been working on parts. If I change something in a part does it ripple through to all the other parts for example

should I be transposing the whole score first before going into parts?