Hey Wes,
were you able to solve this?
Is this an "insulated incident" or is this stuff still problematic in other apps, but maya?
I get a bit frustrated and hold myself back from 3D a bit - I´ve found my way into blender (was hard enough), tried Modo, got my hands on Zbrush for a while, tried Hexagon, Voidworld, 3D Coat and now it seems like "back to maya"... makes my head spin a bit

So I would be glad to finally find a 3D modling app to stick with for the future, to do complete work in and most important - to work 100% with export to unity and SD/SP
Anyways, I made a 6x6 segments cube (in Modo), assigned 5 Materials to different poly-areas and exported as .fbx with no additional settings... imported in SD 4.3.1 (forgot to update my USB-Stick-Version^^) and all material-IDs show up in the baker-dialog, with right face-count and color.
Baking UV to SVG with Material-ID Color works, also...
Kind regards