The topic can be closed. I've found what was causing the issue. It's the Near Death Experience trait that makes AP unable to replenish itself. When I got rid of the trait, all started functioning perfectly. Thanks.
Not sure what is causing this bug. Everything else seems to be fine with the game. I've followed Ess' guide and did all the steps necessary. Here's my modlist and loadorder. Modlist Loadorder: I hope someone can help, thanks!