After further testing today. It was bugged until I swapped Subclass. I was running Solar Hunter with YAS and no weapons were proccing stun mods. I switched over to Void Hunter and then they started working again. Swapped back to Solar build again and they continued to work. Leaving this up because it was mad annoying and seems like others may have been having the same issue with Artifact mods as well. Try changing subclass and then changing back and re-test. Either way this is bugged and needs to be looked into by Bungie.