As reported by trombonechamp: http://www.musescore.org/en/node/2881#comment-6919

1. Open the default Promenade score
2. Drag a 6/4 time signature onto measure 15
3. Drag a 2/4 time signature onto measure 14. Notice that the 6/4 time signature is ignored, and all of the measures after are turned into 2/4 measures. See ignore_64.png
4. Edit > Undo. Note that the music will flow across measures that are the wrong horizontal size, disregarding the barlines. See music flow.png

(Tested using r.2133 nightly and 0.9.5 stable, Windows XP)

Workaround: After steps 2 above right-click on the empty part of the measure and select "Measure Properties". Change the Actual duration to 2/4. Continue with step 3 above.