I got this back from Akai support, and thought I'd post here for others to find at a later date. I haven't had the chance to try it yet, but will let you know how it goes. In the meantime, if anyone has anything to add, all comments gladly received!
Akai: "The Transport needs to be configured in X3:
Working through this whole section enables the Note Repeat, the Transport Controls and Sonar.
On the MPK, do the following:
Press Global, then arrow right to MIDI Clk. Set that to external using the knob, then press in to confirm. Then press the right arrow to the Globals Save page, then press the enter knob.
Press Preset twice.
Load the Sonar Preset.
Press Edit.
Press the Play button.
Press in on the knob.
Make Sure this is set to MMC.
Press the Enter knob to confirm.
Press Preset.
Press the Right arrow > button.
Press in on the knob to save.
This sets up your controller. The rest of the configuration is in the software."