In Maya,
I am having the same exact problem described above, the connection going from the PSD file to the material looks like one connection but when I hover over it it says it has 2 connections .Color and .Transparency. I can delete and reconnect or open connection editor and tell it to break the transparency connection, but everytime I update PSD texture. It goes back to both .Color and .Transparency connections. Yesterday I was updating without this problem, but today I can't seem to figure out what happened.

Could it be Photoshop?
This problem might be coming from Photoshop. Yesterday I was using textures from a 3D texture CD, this morning I downloaded some textures off the webpage CGTexture, and I've been cut and pasting these textures. Am I overlooking some setting when I save as in Photoshop. What changed.

Why is the transparency option setting everytime I update PSD texture?

Thanks for any help.