I just noticed that If I have Final Render materials on my objects and add them to the MATTE objects that Krakatoa will not recognize them.
If they disappear, that probably means that Final Render materials report an alpha of 0, meaning they are completely transparent. Krakatoa tries to handle (semi-)transparent matte objects and a couple common materials really mess that up. The built-in 3ds Max Matte material had the same problems until I special-cased it away. This might be another thing I need to specially handle. Unfortunately, even special casing these materials will fail if they are nested inside of a multi-material, or a blend material, or anything else really that will obscure their actual identity.
As the rule of thumb: Standard Materials are the way to go when working with Krakatoa.
I’m testing this right now and fR-Advanced materials work fine as matte objects. What materials were causing you trouble?