Don't know if anyone is still looking for an answer, but here's what worked for me. If you're using Mod Organizer and used it to install the plugin, you either have to edit the plugin inside of Mod Organizer's Mods folder, or remove it from there and install it under Skyrim/Data/SKSE/Plugins. I moved mine, and it worked. You will still need to edit bUsePerksAtLevelUp=0 to =1, but if you've already done that and you used Mod Organizer, this should do it. Hope this helps someone.