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.