Gamecube skipping Progressive Scan. Viper Extreme / Swiss

I installed a Viper Extreme. I noticed that my games stopped asking me if I want to use Progressive Scan. Booting a game directly from disc in Cobra, or directly from disc in Swiss, both result in skipping the check. A game did ask me for Progressive Scan, when I changed Swiss to force it.

Any ideas why it is now skipping this check?