Whoa! I finally did it! The Cannon Fodder WHDLoad version started to load at last! The problem was that I had to uncheck the "Use Faster Chipset" option, which was preventing the game from running for some reason.
Use faster chipset was added as an experiment for those requesting options for WHDBoot games, (previously default setup was always used). It's can causes quirks though and you should always start with it set to off and only turn on if you experience slow performance on a heavy blitting game. This would also explain the flickers in the ADF version BTW
