Goolge won't have anything against Magneto as it is a very widely used platform and there would have been a lot more people asking this sort of question if Google suddenly decided it didn't like it. I would have a look at all your sites link profiles and see if there are any clues there? I would also look at your sites architecture/structure and see if you have a duplicate content issue which can be common on e-commerce sites. For a more in depth insight you will need to share your sites with the community.
If you haven't already I would run your sites through http://www.opensiteexplorer.org/ for clues
