Actually, transposing notes in the BBM Editor is really easy as you can right click on the name of the notes and choose to move them where you want them. You can do a whole song in a matter of minutes.
But, have you exported these midi files from a Windows version of the BBM? I know I can’t do it with any version of the BBM in Windows. We do have Macs here though which export the files properly. I was getting long blue lines like you have here.