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Well, I downloaded the demo of this useful program today. When I loaded a model that had a large amount of meshes needed for DBClassic style bone animations, some of the claws on the left hand articulator of the robot didn't show up. Is there a maximum amount of meshes or polygons that the program can handle. The model I was using must have had close to 41 meshes, and around 1024 faces (yeah, that's alot). Is that what the problem is?

Yeah. I think so!
At least I have bought CharacterFX, and founs out that if I import .obj-files, then CharacterFX messes the model up. But when I import the model as .3ds, everything works out just fine, except that I have to keep the faces in my model at absolute minimum. I tried to begin with to import the model with more than 1000 faces, but only got an error message (In german in fact), but when I lowered the faces to around 800 everything worked fine.
My advise to you is atleast import your models into CharacterFX as .3ds, and with as few faces as possible, then everything should work fine. Avoid importing your models into CFX as .obj.
Hope this will help.
cheers