Nice! By the way, Logic has just been updated to 9.1.3 (Logic updates are like London busses at the moment!) - for non-UK residents, this phrase means: No busses turn up for ages, then multiple busses arrive simultaneously!
... oh and my point it, 9.1.3 automatically fixes the Hyperthreading issue and gives options within Logic on how you wish manage multiple cores in
Logic Pro > Preferences > Audio
Is the Novation sending duplicate messages for Stop? Like when you press Return to stop during playback, press it again to return playhead to beginning of project?