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This occurred to me today when i imported a .lwo obejct saved into .mxs from Cinema. being in hurry i had not changed all the materials before saving, so when i opened studio, there were some layers with more than one projector. Then i canceled all the multiple projectors and then assigned a new one. First of all its channel assignment was not 0, and then i wasn't able to attribute a unique material to the whole layer. Those parts that before where linked with another material couldn't be assigned to the new overall one.

Did you look in the triangle list of that object? Do some triangle groups appear? If they do, you can delete them so that your new material is applied to the whole object.

Already done, but no triangle group is shown. Tried to hit merge anyway (hoping they were just hidde) but no way...
Maybe cold be useful to know what is my workflow:
Modeled in Archicad, imported in Modo, layered there on a material basis (but this time i haven't changed the materials itselves, only organized layers), exported as .lwo into Cinema (did this because by exporting into .obj format the layers take the name of the parts, that in modo are not editable) and then created .mxs.
I have repeated the process again but this time i assigned to the whole model the same "default" mat, and this time the things went as they always did. So the problem lies into geometry-mats relation, i guess.

Any new about this, mihai? I am scared by things that happen so unexpectedly. Can up the scene, if you need...