Copying Between Transposed Scores

I couldn't find a forum post that covered the exact problem I'm having here:

I have a classical score which I have transposed from Cm into Dm using the transpose tool.

I am copying parts of this score into a brass band template as I make an arrangement.

The brass band score has also had this same transposition done to it previously since I changed my choice of key half way through the arrangement.

For some reason, the note sound is changing between documents. Eg, I copy a concert D over, and it is suddenly sounding as an Eb. Neither instrument is a transposing instrument. As far as I can tell toggling the concert pitch button does not help.

Am I being a dunce? I assumed the transpose tool was for quickly changing the key of the written music, not actually applying a permanent transposition to the instruments.