Trouble with Ruleset Replacement

Where are you looking for the skills? When you import new skills into the backend (by replacing the txt files), you simply give d20pro the ability to use those skills from then forward. If you were to open an existing creature, it still has its old skills - many of which still work in pathfinder but many don't. It doesn't convert the skill list over.

So a creature may still have listen/spot listed in its trained skill list and that should be changed.

If you select a creature and hit K or right-click and choose skill, you should see skills now categorized as: athletics, combat, knowledge, rogue, social, other, and all - click on Social and you should see Linguistics as the second skill in the list (that's unique to pathfinder).

Likewise, if you Edit the creature (E) and go to its Skill tab, you should see only the skills its trained in, but if you click Add, then you will see the full Pathfinder list. Click the screenshots below for a better view.

If you do not see these then you have likely copied the files to the wrong folder or haven't restarted d20pro.