Key Change question

My apologies if this question has already been asked. I looked around but didn't see anyone with the same problem.

I'm using musescore version 1.2 for Mac. My problem is as follows:

I'm arranging a piece for big band. I used the big band template when setting up my score. I'm doing all my note entry in concert pitch (Concert Pitch checked under the Notes menu), which has been working out beautifully. The first portion of the piece is in C, and when I uncheck "Concert Pitch", everything is as expected: B flat instruments switch to 2 sharps, E flat instruments switch to 3. Re-check "Concert Pitch", everything goes back to the key of C. Awesome!

60ish or so bars into the piece, it changes to A flat. I dragged the little four flats icon over and dropped it into the score on each line. Everything looks great. Awesome!

Here's where it gets not-so-awesome. Uncheck "Concert Pitch", and the correct new key signatures display just fine. However, the originals are changed. My E flat instruments display an original key signature of six flats, and my B flat instruments now display an original key signature of four sharps. WEIRD!

So I tried it the other way, without "Concert Pitch" checked, making the appropriate changes at the appropriate bar. When going back to concert pitch, it again changed the original key signatures of those parts, but then correctly displayed the new key signature.

How do I deal with this?

Thanks,
Jeff