Just a quick comment about that Layout bug (and fix).
I found that just checking that box to reorder the layout won't necessarily work. At least, it didn't at first for me.
From what I could tell, Stepmania would change resolutions and then change it back, BUT windows wouldn't necessarily finish the process of changing the resolution before Mala got control, so the "redraw" process in mala was happening based on the wrong screen resolution.
To fix it, I created a little BAT file to run stepmania, with a WAITFOR of a couple seconds after stepmania executes.
Then I pointed Mala at the bat file to launch instead of the stepmania.exe file directly.
That way, when stepmania exits, it waits for a few seconds, which gives the screen res switch time to happen, and then mala gets control, and it redraws properly.