Clefs not matching between score and parts

Please be gentle, non-expert here. My 11 year old daughter is just finishing off her first piece for orchestra on MU4. She has an issue with the parts not matching the score on piccolo, bass clarinet and tenor sax. The common factor is that for each of these instruments the score uses a treble clef to be played either an octave up or an octave down. However, on the parts the notes show either an octave up or an octave down on the stave, compared to the score (incorrectly). But when you play back the part, it sounds the same as the score. We have tried regenerating the parts, but it just does the same thing. Any ideas for an explanation or a work-around? Thanks.