I just updated to mame 162 and Mala is working just fine.
However I only have a single games list and run mame roms, I don't have a tree, multiple emulators, or anything else.
Mame and Mess have been merged so that it's one executable now. Trying to figure out how to run some snes roms at the moment and see if I can get that working with Mala. If anyone has done this, report back because I'm not finding it that easy to dig up info about how to do it.