Transposition error

Background:
The music is written for C-Clarinet. I scanned this into Smart Score to generate an xml. file for subsequent input into MuseScore. The final .mscz file seems to be correct Test.mscz
Problem:
I then tried to transpose this up one tone in order to be played with a Bb Clarinet. The music was written in the key of Bb so the transpostion should be up one tone and written in the key of C. The result was erroneous as you can see. Test_transposed.mscz
Is the mistake mine or has the xml. file generated by Smart Score been corrupted in some way thus making proper transposition impossible? Looking forward to your reply a.s.a.p. since this is part of the Mozart Mass in C Minor which we hope to perform in a couple of weeks time!

John McWilliam