I've given up trying to work on DDSes in their native format. Transparancy doesn't show up correctly, and I'm forever getting odd, seemingly random shade changes when I save files. Instead I've taken to using
DDS Converter 2 to convert DDSes into PNGs and vice versa. While it warns that PNGs aren't the most efficient intermediary (I think TGAs are) PNGs display transparancy correctly in Photoshop CS, so they're far easier to work with.