As I use Opera every session, but I don't want it to autostart, because that would be just one more item to slow rebooting. A little patience to wait for it to start wouldn't hurt.
EDIT:With Firefox in the Startup folder, did you run Autoruns, and check for duplicate entries?
EDIT: Another program that you can use is StartupCPL: http://www.mlin.net/StartupCPL.shtml
It is not as complete as Autoruns either, but easier to use.