The way to do it is here: http://www.captainsim.org/yabb2/YaBB.pl?num=1282647312/1#1

If you leave them as .BMP they work fine (you don't need to do anything with them). If you change them to .DDS you need to flip them vertically. To do this in DXTBmp.exe, from the menu select Image > Flip Image and Alpha
I recommend Flip Image and Alpha just in case the texture does actually have an Alpha channel that may appear as empty. I think it's also a good habit to get into, otherwise you might forget to flip the Alpha in a texture that actually does have one that needs to be flipped.

Mark