First at all, ISO itself cannot store protection information. So image was destroyed in the very moment when you made ISO from it.
Another bad part about ISO is that it cannot store multi-track discs too. Usually it's the problem with the older games, where data and music/sound contained in the separate audio tracks.
So in the future I recommend
Daemon Tools Lite. It totally can support almost any image type, and I believe that it can made "right" protected images in MDS/MDF format.