transposing clarinets and horns

In order to understand, we'd need you to attach the scores you are having probems with, or provide precise step by step instructions to reproduce the problem from scratch. But first - are you familiar with how clarients and horns normally transpose? If a score is in C overall, then clarients would normally show key signature of D, and horns would show G. I'm assuming you have the "Concert Pitch" button enabled for your first movement and that is why they are all being displayed in C. In the second movement, if the Concert Pitch button was *not* enabled, you should be seeing D and G, not Bb and F - or, of course, C all around if Concert Pitch *is* enabled. Are the actual piches what you exepct and just the key signatures wrong, or are both wrong?

So again, we'd need to see the actual score (the MSCZ file itself, not just a picture of it) to really understand. If you at one time edited one of these scores with an experiment pre-release version of MuseScore (eg, one of the beta or nightly builds) then it certainly possible a bug did something to your score and you'd need to transpose it manually to fix it.