As far as I understand, the MIDI specification only thinks of the keys as numbers, and there’s no standard that says which octave the keys center around.
Here’s a thread on KVR about this: http://www.kvraudio.com/forum/viewtopic.php?p=4268131
In some programs like Logic, you can choose which octave the piano roll is centered on (as in automatically transposing everything).
If it’s a problem for you during scoring that everything is shifted by an octave, the only way I can think of is to enter notes at the right position, and set each track to transpose by an octave (in the track properties dialog).