Any difference in flavors between .fbx files generated by Maya and this by 3d Studio Max as a known issue?
When I import models into Unity that were created in 3DS I get alignment weirdness. I found it necessary to import into Maya then export out again.
Also, 3DS is running on PC, I have Maya on OS X.
Thanks,
r.b
Im not sure of any major differences, but as far as I know, max and maya use different world axis-systems. In maya Y is up, while in max Z is up. This is probably what causes your alignment weirdness when you export directly from max to unity. I guess the fbx`s axis is corrected when you import it into maya and then into unity, as both use the Y-axis as the up-axis 
It could be that because maya is so tightly integrated into unity, that your alignment problems are solved too, but I don`t know.