I have seen this problem before, and I don't know a perfect fix for it. I had to apply the texture myself. I can go through the steps of applying the texture, but you may already know all this.

Select the object (RMB) and press F6 to get the texture controls. Click the Add New button in the Texture Panel. Then you will be able to choose a Texture Type. In the drop down choose Image.

Two new panels will appear. In the Image panel,click the Load Image button and select the texture.

Go back to the Material buttons (F5). In the Map Input tab (far right), change it from Orco to UV.

Now you should be set. I will do some searching around about the problem. Version 2.42 will be out in a week or two and it might be fixed then.

If this does not help at all, maybe you could make the .blend or .obj available to me I would be happy to help, or maybe someone else will post a better way to fix the problem :)