Gain vs S11 (Antenna Engineering)
An antenna's realized gain is the antenna gain reduced by power lost to reflections at the antenna feed. The antenna gain is the product of efficiency and directivity:

$$G_R = \left(1-\left|S_{11}\right|^2\right)E_A D$$

If \$|S_{11}|\$ increased, but realized gain also increased, that implies that one of the other factors improved. I would normally think that since you didn't improve the conductivity of copper or reduce the dielectric losses of your substrate, the efficiency term most likely didn't change much. So it's most likely that directivity improved.

But something still doesn't quite add up. -20 dB is really a very good \$S_{11}\$ magnitude, indicating a very well matched antenna. And the \$D\$ term is always greater than 1 (since any change from perfect isotropic radiation increases \$D\$). So the -12.5 dB realized gain in your first measurement indicates a very poor efficiency value. 

It seems likely there is some subtlety to setting up the realized gain measurement in the simulator. Perhaps some signal is being reflected back into high order wave guide modes, or into guided waves in the board substrate, and these are not being measured as part of the reflected wave or the radiated wave, resulting in very poor efficiency.