whats up with the progressive? lol every game that supports progressive will ask for it i dont see what is your problem with it, the forced progressive setting doesnt change this even if you use force progressive on games that dont naturaly support it, the message wont appear becuase the game doesnt have that message, if that message appeared its becuase the game supported progress naturaly being forced or not.
The message only appears if the game naturaly forced progressive see here, nothing to do with nintendont.
http://en.wikipedia.org/wiki/List_of_Nintendo_GameCube_games_with_480p_and_16:9_support
played rogue squaron III for like an hour, did 6 missions and never had long black screens before cutscenes at all, are you using an SD card?the only change is that nintendont now mimics the gamecube disc read speed so nintendont is on porpose slowing down a tiny little thing on loading becuase manny games had issues with the speed being too fast and desynced the music.
Also what are the dev main credits on rogue squadron II and III?