Is the magenta area in your rule a regions layer? If so, delete it: regions are not needed in 1.9+ and are only included for backwards compatibility with pre-1.9 rules (before the special Automapping tiles existed), and they trigger pre-1.9 Automapping behaviour. I think you’re actually running into the old behaviour that if a tile is empty on all input layers (and I guess the special tiles get ignored in this mode), it counts as “Other”.
I just set up an equivalent rule to yours but without regions, it worked correctly in both scenarios.