Hi Dan,
This seems to be in issue with Showcase and the way it's importing and exporting the files. Your best bet is to head over to the Showcase forums and ask the devs there. You can find the forums here in the Area, just down the hall to your left (these forums are dedicated to the FBX plug-in for Maya and Max, softwares like Showcase implement the FBX SDK in their own way, that is why it is best to ask the Showcase devs themselves):
http://area.autodesk.com/forum/autodesk-showcase/general/To make sure though, I'll ask you to do one test. If you export your model with materials from Maya, and then re-import that same model back into Maya, what are the results? If the results are the same, meaning everything is fine, then that tells us the plug-in is working and the problem does lie with Showcase.
Cheers,
Carlos