This stuff is all after my time, so I have no idea how FL Studio works, having only borrowed it and used it once before I went back to where I came from. Supposedly though, there should be an Options menu with MIDI settings in it, you can set the input to your, presumably, USB-MIDI wire there.
Be sure you have the MIDI IN cable connected to MIDI OUT on the keyboard and that you set the channel in the keyboard's MIDI page correctly, KBCH is the one for output. Past that you're probably using VST's or something and you might need to set them individually, I've no real experience there either so can't really help on that one.
There is another thing, try power cycling the keyboard - sometimes an application sets it to "remote control" so the keyboard on it won't work anymore, it is easier to power cycle the instrument if you don't have quick access to the controllers to set it back. Cakewalk 9 does this to any synth I hook up and it's annoying... Mostly as I'm sure it can be disabled but I can't be bothered to look in the menus, not that this helps you any in FL 12, but the same thing might be happening I guess.