Scores made with 1.3 get messed up in 2.0 RC

Actually, the score has issues in 1.3 too, although they are partially masked. Try removing the line break at the end of measure 8, though, and you'll see things are quite messed up - there too -- stems go totally.

The problem has to do with the beams that are used across some of the barlines. Both 1.3 and 2.0 support this, but neither work properly if there is a line break between the measures. It looks like perhaps there used to be a beam across the bar here, it caused a problem, and you (or whomever created this score) tried to undo it or otherwise repair the damage, but somehow things some part of that cross-measure beam remained to cause problems in 2.0.

The fact that beaming across barliens does not work across systems (line or page breaks) is the subject of an open bug report at #16278: Beaming notes over barlines and line breaks. Meanwhile, you set things back to normal in this measure by selecting it and double clicking the Auto icon in the Beam Properties palette.

BTW, this score also has a problem in that the crescendo line and and slurs have been extended improperly. It looks like they were entered originally as short liens then simply dragged with the mouse to make them longer, rather than anchored to the correct notes with Shift+right/left (arrow keys). That makes the layout "fragile", meanng it won't be guaranteed to look the same if the layout changes (eg, if you start changing where line breaks happen, or if a different version spaces things notes differently). The voltas (1st & 2nd endings) appear to have been extended correctly.