I'm just shooting in the dark here.
1. You create a material, and assign texture map to it a file texture that has alpha information in it.
2. You can not move the slider in AE for the material.
If that is the case, it is simply because maya automatically assign transparency of the image file (base on alpha) to the material.
You could see that the map icon change into connection icon in the AE. Simply break the connection and you regain control of the transparency slider.