Hi Klas,
happy to hear that you´re already having fun with your Zaquencer!
About the problem, I can only offer rather general troubleshooting advice.
For example you could try triggering your Midi channels with another Midi source like a keyboard, if you have one. Then you could look at the Zaquencer´s Midi data with a program like “Midi Monitor” (on Mac): http://www.snoize.com/MIDIMonitor/
This way you can see which side the behaviour originates from.
If the Zaquencer sends on the correct channels, it might be connected to Logic´s midi routing. As I wrote before, I didn´t use Logic X before, but it might have something to do with the environment (if that still exists). I found Logic 9´s Midi routing a bit intransparent back then…
Maybe other users with more Logic X experience can chime in as well?