Yep, definitely. And remember, the lighter parts of the alpha layer will appear shinier than darker parts in-game. Having no alpha is the same thing as having a completely white alpha layer meaning everything would appear equally shiny, which is what you were experiencing.

@Ginev: Just to confirm that the shininess isn't the result of the new shaders, are you using proper specular map textures? (i.e. grayscale textures that go in the alpha layer of both your diffuse and bump/normal map .tga files similar to what most stock weapons have)