First off, I tested with only this mod and penetrating strike applied correctly to both swords and axes, so this may be beyond your scope.

I am playing a custom modpack and was unable to apply penetrating strike to a sword. It does applies correctly to axes however. Looking at "src/main/java/net/Pandarix/betterarcheology/enchantment/PenetratingStrikeEnchantment.java", the EnchantmentTarget line you use is distinct from all the other working enchants in the modpack: the others using EnchantmentCategory or specifically defining instanceof. Not having made a mod myself, is there a benefit to EnchantmentTarget or could EnchantmentCategory fix my issue?

Thanks for making this modpack, the chicken skeleton being a dinosaur and the ocelot being a saber tooth made me laugh.

Corrected in commit a1cd77a
Will be added in 1.1.1.
Thanks for reporting!