2 UV Sets

I created a model in Maya that has 2 UV sets. One for the colormap and one for the lightmap. I brought the model into Unity and I applyed a Lightmapped/Bumped Specular shader to the object with the two uv sets. I loaded the textures into there correct positions but its acting like its applying the textures to the wrong UV sets. If I flip the textures around it applies them to the correct UV sets however the colormap in the lightmap channel looks wrong. Not to mention it houses the spec map in the alpha channel so this is not going to work. Is there somthing I am missing here? how do I make Unity apply the correct texture to the correct UV channel/ Is this somthing that needs to be set up in Maya?

Because Unity has speculars bind to alpha of materials they use the same UV set of that texture, no way to escape this unless you modify the shader itself (should be easy anyway).

On why the maps look on the wrong UV you should post at least a screen… are they swapped (UV1 in UV2)?
Also, in example, in Max they are named UV1 and UV2, while in OGRE it names UV0 and UV1, so watch out for these things!

Solved. I found a button on the far right top that says select and in the inspector window that poped up there was a swap UV checkbox. This solved the issue. In maya you can name the UV sets anything you want so currently they are called map1 and bake.