Ah, these are 2d graphics, I thought you were talking originally about 3d. The 2d graphics support the alpha channel for masking purposes. What may be happening is your conversion to bitmap (or is it jpeg) is removing the alpha channel (not sure if BMP supports transparency). Get the dds plugin for photoshop, or get gimp with the dds plugin. Not sure if PNG supports alpha channels, but you might try converting the dds to PNG or TGA instead of bitmap. It's also possible that you are stripping out the alpha channel when you convert to dds, you need to save as DXT3 (default for the game I think) or DXT5. DXT1 doesn't support transparency.
Google dds plugin and you should get the nVidia plugin listed for photoshop.
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