It is no surprise that there is a difference. The Photoshop GIF saved at 90kb is going to look better than a Flash GIF saved at 49kb.
You need to address your compression options. ... and this would be best done in the forum for that particular software.
Ya if anyone will respond in that forum. I'm starting to think that Adobe doesn't allow you full compression control in flash. The only real option I could find is "losy" or "losless". Besides loseless that I've tried every combination in published settings and nothing can compair to the clearity I get through photoshops animation tool (then compressed to a gif via "save for web and devices").
If someone could tell me or show me how to make this work, I'd really appriciate it.