You got me there. Read your post too fast 
Did you check the Mayflash website and make sure you're on the latest firmware?
Does Windows see it as multiple controllers? I think you can check with the Windows controller calibration tool: https://support.xbox.com/en-US/xbox-on-windows/accessories/calibrate-xbox-360-controller-for-windows
Does this happen in 5.0 stable, or 5.0 dev builds?
Does this happen with official Wii U Pro controllers as well as the Hyperkin Procube?
Did you check the Mayflash website and make sure you're on the latest firmware?
Does Windows see it as multiple controllers? I think you can check with the Windows controller calibration tool: https://support.xbox.com/en-US/xbox-on-windows/accessories/calibrate-xbox-360-controller-for-windows
Does this happen in 5.0 stable, or 5.0 dev builds?
Does this happen with official Wii U Pro controllers as well as the Hyperkin Procube?