The emulator is slow, buggy and renders a lot of BS. You can't expect to get proper results from it.
About the missing materials...yes...i hoped that nobody will notice...
It's a problem with the way how jPCT handles solid colors. It creates colored textures for all these colors. But textures itself won't be serialized, only their names are. When loading the serialized model, jPCT-AE looks for textures with that name in the texture manager and because it can't find them there, it will use a white dummy texture. For now, you have to create these color textures yourself and add it to the texture manager with the proper names before loading the model. This "process" involves to scan the log of the loading process (of the orginal model, not the serialized one) for output about textures being created like "__3ds-Color:123/234/96". Then create textures with that name and that color (in this example: red=123, green=234, blue=96).
Yes, it's a pain...it's a better idea to assign a real unicolored texture instead in the modeller. Or wait until i've added support for this to the DeSerializer.