I have a KORG M3, and I have the exact same problem. Almost all KORG synths even the later ones only outputs MIDI System realtime messages but not the Midi Machine Control (MMC). I was rather disappointed that I was double whammied by MMC being unsupported on M3 and MIDI System Real Time clock unsupported on the Logic... the classic square peg into a round hole problem.
As pointed out in other posts, the MIDI system realtime message IS sent out from Logic. It just does not receive it. You do have to turn in on though in the project sync option.
Now I know for sure that only option I got is to slave the M3 to the Logic. Fortunately I don't own any other legacy so I can work it, but I don't know what I would have done if I had a bunch of old stuff... all SMPTE conversion boxes are really expensive!
From the post I did at Apple's Logic Forum and other places, the general consensus seems to be "What are you talking about! All my stuff supports MTC now." Yeah, right!