Multimatte on multi-sub object materials

[tricky]

Material IDs don't seem to work within MultiMatte.

[jordanw]

Thats because its looking at the Material ID Channel (or Material Effects Channel) not the Material ID as set per polygon or by the Material Modifier. Very similar naming, I know!
The Material ID Channel is in the material editor and is the drop down of 16 numbers (no one would ever need any more that 16!!).