If you used the transpose option in the Notation Window Options, that is only a visual transpose, typically used for transposing instruments (e.g. sax, trumpet..)

There's an easy way to tranpose the pitches of a MIDI melody under the main menu: Melody | Edit Melody | Tranpose...
There are actually keyboard shortcuts for melody octave up or down (CTRL+ALT+1 and CTRL+ALT+2)


Andrew
PG Music Inc.