Soz just realised didnt actually tell you how to fix the prob lol.
In the hypershade select the offending texture and right click > graph network, it should then pop up in the bottom part of the hypershade. There may be a couple of arrows connecting the texture node to the the materials shader node. One of them will say something along the lines of 'transparency. woteva the file is called'. If you delete this it should show up in the scene.
If not I'm not sure what could be wrong I'm afraid.