Quartus doesnt recognize my FSM as a FSM

I always use one process state machines as I find they are easier to write. They are perfectly recognised as such by Quartus, even if I don't follow strictly their recommended style (http://www.altera.com/literature/hb/qts/qts_qii51007.pdf).

Your problem could come from the fact that you register a whole bunch of signals in the first process and have all your signals retain their previous value in the second process. I hope that Quartus is smart enough not to generate latches from your second process description.