After Effects CS4 could export animated GIFs, but 5 and on apparently can’t. I’d export an TIFF sequences, making sure to export RGB + Alpha, then import that into Photoshop, and then export the GIF from Photoshop. Not sure Photoshop’s GIF support parameters, but as Darby said, GIFs can support on/off alpha channels.
Benjamin Ausmith
Post-Production Assistant
Monadnock Media, inc.