I think it all ties back to pesky souls and the writer's interpretation of how that all works, and that Joss never cared about continuity or good storytelling if it got in the way of his grand scheme.
The mechanics of the chip were never really spelled out. It couldn't really be a soul detector so technically it could only be detecting life signs which would mean all animals. Arguably it could be set to determine intent on Spike's part in which case human could be the default although that would have stopped Spike from hurting Buffy, so perhaps the Initiative had identified some sort of demon gene and when Buffy came back from the dead her demon gene was activated?
I'm just going to go with artistic license and the writers changed it to suit.