Thanks. Turns out my Mbox's breakout cable is broken. A midi to usb cable works in Pro Tools and Fl Studio. I tried a 2nd pair of midi cables but those also didn't work. So my guess is that the breakout cable and not the word clock midi s/pdif connector on the actual Mbox is broken.
I wasn't sure which one was correct under Pro Tools midi studio setup (external or control) so I just added them both just to be safe.