Djefferson,
I'think your probleme occurs because the setup/layer definition/association may be not well defined.
Be sure to associate with TOP LAYER the corresponding layer for SILKSCREEN,PASTE MASK and SOLDER MASK ans ASSEMBLY in the associate menu.
I' have notice that the add/delete layer in padstack editor do not works (sometimes) if layer definition/associated layers is not well defined.
Sometime you will have to save,exit and reload PCB to see the difference.
I'have tested different configuration,when the layer definition is OK all option to achieve changes in padstack editor works fine.
Vincent.