Jeremy i can confirm what you described about the layer material assignment.
in fact i was just browsing my mail to look for my description concerning object based assignment from back then, and found a draft i probably never sent you
i"ll just paste the important part as there are a few people here, and it also refers to blocks like kami's problem.
The materials dissapearing, it is not that they are deleted, but the objects loose the assignment.
it is shown correctly in the rhino material properties tab, but in the maxwell one they are gone.
But they still do exist in the scene.Also, if in a concerned maxwell material i had selected a texture slot, so that the texture was displayed in the viewport, the corrupted "rhino" version of it will contain that texture.
(so eg. sometimes i see objects rendered with blue normalmaps as color)
It is not related to blocks, but it happened to objects inside embeded blocks too.
linked blocks i use with imported materials, so probably they are not affected.
also i never loose the actual "plug In" flag, the material is simply vanished from the maxwell tab.
and,
not sure if i ever mentioned that the texture loaded in the resulting rhino material will not contain the original texture, but a path to a "proxy" texture! this will be revealed if i
uncheck the plugIn box to display the corresponding rhino material.