Leeneia..

you raise 2 semitones in the transpose section, I think you've found that..... but it won't sound the transposition until you go into the midi ('staff properties' ' midi') and reset the transpose there to '0'

the accitdental are probably because of 'enharmonic notes' which the program is not sure what to do with...

I can also help if you want to send the file... pevenden@home.com