it appears that some specific passes in Maya require material adjustments. So if you export an assembly then the set of passes established at that time is important. Adding such passes later and then load assemblies exported before the adjustment may not work.
One solution would be, to keep the actual materials in the master scene and export assemblies only with references, but not the material/shader itself, as Bart suggested. The "export assembly" functionality in Maya seem to have trouble to respect the custom export filter (a bug?) So you may need to edit the .mi file instead.