Hey Deteez, looks like I spoke too soon, I'm having exactly the same problem!
Preset 9 works fine with Ableton when first loaded, but after switching to any other preset then switching back none of the pads work as clip launchers. Sometimes they seem to do nothing, and sometimes they seem to switch to just sending midi notes. Sometimes the transport controls still work as normal, sometimes they just send midi notes too. Even starting on Preset 9 and switching to the step sequencer, returning to the clip launcher stops the pads working.
Any changes I make on Ableton itself updates the LEDs on the QuNeo for the clip launching, so it's still connected properly. Switching back to 1.1 works fine with the older Ableton Midi script, but again, the new features included with 1.2 are so useful that it'd be much better if this can be fixed. I guess this is a problem with the newer Midi script for 1.2?