RE: Error: Cannot reconcile.
>> "In March, the NZ Commerce Committee recommended that computer programs should not be a patentable invention."
>> "The rulebook will eventually allow inventions that contain embedded software to be patented, he said."
There is no problem there.
Suppose I submit a patent for (just plucking something out of the air) "An improved method for temperature control of living spaces" - and give the apparatus a description along the lines of "The apparatus control the output from the heating system based on the temperature of the internal space". Anyone with a few brain cells switched on may recognise that as a thermostat !
Now, I could make it an old fashioned mechanical jobby with a bi-metallic strip etc, or I could make it an enhanced functionality type with some software running on an embedded processor (as many are these days). Indeed, I may add to the description things like "... and taking into account the external temperature, the initial temperature of the living space, and the the normal rate of rise of temperature so as to calculate an optimal switch on time prior to a user set desired occupancy time for the space". In the latter case, I've described a more sophisticated device that will adjust the turn on time of the heating so as to get the room up to temperature for the time set by the user - it switches on later in warm weather and earlier in cold weather. For that, embedded software would be "almost" certainly required, though it could just about be made to work by mechanical means.
Yes, I know both are now commonplace and not patentable any more, I only offer it as a simple example - just assume for the sake of example that there were no prior art.
The invention AS A COMPLETE SYSTEM is patentable - ie a thermostat with specific functions and capabilities enabled by certain inventions (ie algorithms). The software embedded within the device is not itself patentable - though it can be protected by copyright.