The stuff listed in Grey (Jog/Lock for AI Knob, Add Inst Track, and so on). Those send out specific commands for Cubase only.

If you are using Logic there is a different method. First go here and download the Yamaha Steinberg USB driver and the Reference Manual.

In MX, go to UTILITY/REMOTE and set the Remote to "Logic" and press "Store" (page 68 in the Reference Manual). I avoid setting this up under Logic's Control Surfaces area since there is no MX template (and trying to rig it there can sometimes not work).

I find the most flexible way to set up the Remote Control surface is under "Key Commands" under the "Logic Pro X" menu. You can then set the Stop and Play commands there as long as you have the MX49 Connected and Logic "sees" it.

You can Set Up the 6 buttons on the front panel (Organ, Guitar, Bass, Strings, Brass, and Sax/Woodwind). These 6 buttons are customizable in both Cubase and Logic (they send note on commands). You can set them up anyway you wish under Key Commands/Global Commands, then select the command you want and select "Learn New Assignment" in Logic. I have the hardware MX buttons "Stop" and "Play" for the two Stop and Play. As long as you have the DAW Remote button on these commands will work however you have the configured for your flow. Since they send on Port 2 they will not affect MX tone generator communication which happens on Port 1.

See if this helps you.

Also there is a video here that shows how to set up in Logic on Logic 9 and the original MX. This one gets into Audio MIDI set up and shows how to set up here as well.