@Chris Scott:
If I recall correctly the Alpha Floor functions with A/THR OFF, but it will not function if A/THR is *disabled*, if not in Normal Law, or below 100ft RA. I'm not sure about the Mach limit** - OK465, would you have a reference handy?
One thing that struck me when I read the airprox report was that the A340 Captain said he noted "ALPHA LOCK" on his PFD, which the AAIB took as a misreading of "A. FLOOR". The thought occurred to me that it might possibly have been a misread of ALPHA PROT (from the transient AoA anomaly) and THR. LOCK (from the AP disconnect). Just a thought...
** - I should note however, that in my experience OK465 is usually correct!