The matt grey was the chromium. What you think is chrome is the underlying nickel plating and steel. Too late now, but next time use a weak oxalic acid solution to get the rust off. Oxalic acid crystals are available on the internet. Do a search on these forums for more information.

Don't worry, it's not the end of the world. Once you've polished all the rust off, finish your bike with car wax.