It turned out that it was an issue with the unsigned driver not being installed properly. If the installer is run and it isn't installed, then the bluetooth issue occurs where all bluetooth and keyboard functionality is disabled on the device. When I uninstalled every part of the NI Mate software and drivers, rebooted and reinstalled with unsigned driver installing enabled, the issue was resolved.
Added 30th Sept:
Judging from my tests with my new Surface Pro i5 8GB, it doesn't seem to be able to handle the Kinect v2 for any longer than about 20-30 seconds...keeps dropping out and then coming back on again.
Added 1st Oct:
Just wondering if anyone has had any success with Kinect v2 on the new Surface Pro i5's? I keep seeing forum posts of people using Kinects on older Surface Pros and they seem to be able to do it no worries, however as mentioned above I keep dropping out...