I just got mine working after some effort with tech support. The was resolved by a full factory reset. Something amiss in the system.syx possibly?
1. IMPORTANT Backup! Don't try this until you have backed up with Fractal-Bot. Else you will loose all your patches, settings and cabs!
2. "Clear the SRAM which will remove all presets, user cabs, and system settings (i.e. it will erase your presets, user cabs, and system settings). In order to reset the SRAM on the Axe-Fx II go to the Utility menu on the front panel of the Axe-Fx II and press the PAGE RIGHT button 10 times. This will bring you to a hidden menu with the option to clear the SRAM. After clearing the SRAM, reboot the Axe-Fx II and try connecting with Axe-Edit 3.0."
3. Then restore your banks backed up in step 1. using Fractal-Bot send. Or you can download all the factory patches from here..
Fractal Audio Systems - Support
4. Close Fractal-Bot before starting Axe Edit
Good luck!
W