What type of "rubber" is installed? EPDM (real rubber) or modified bitumen (the rubber that isn't real rubber but people still call it rubber)?
Most likely this is what happened... Previous building owners went cheap and when the metal roof began to leak rather than tear it off, they just installed numerous roofs atop the old metal.
Without seeing the roof I can't really make a suggestion. You can learn more about flat roofing options
and frequently asked flat roofing questions
on my website. If you post some pics I'd be happy to make some recomendations.