I do not use Shake so I have ho idea how it is interpreting your layers and alphas etc.
So, any chance you could package/zip/rar-up one frame's-worth of your layers (raw out of maya) so I could throw them into Fusion or AE as straight individual layers to see if Maya may be doing something against you?
Thanks
Israel "Izzy" Long
Motion and Title Design for Broadcast-Film-DS
izzylong.com