I just had my computer updated here at work. Now when I go to use Photoshop and save a file, the option, SAVE TRANSPARENCY doesn't come up. When I import into Final Cut it it not a transparency but a whole image. THe background won't disappear. Any ideas? Maybe it's something simple short of reinstalling the program?
What file format are you trying to save into? Generally to get transparency you can use PNG, PSD, MOV or GIF.
Also what version of PS are you using? If you use the export as MOV in CS3 that should work to get it easily into FC.