So as title says the weapon Proficiency trait is not working for me. both my characters have gotten it and they still get the +4 difficulty any time i use a weapon that requires it and its really annoying.  

That's ridiculous! Can you show some screenshots of combat checks where weapon proficiency isn't applied? If you can click on the "active effects" panel before you take the screenie, we'll be able to see some of the effects that might be triggering and contributing.

 

If this was a general issue, we'd have heard about it immediately patch 1.1.5.1 was deployed, the wailing and gnashing of teeth would have been audible across the globe! Therefore there's something odd about your situation. Providing as much info as you can might help us to help you. See the post OBS made on reporting supporting information http://forums.obsidian.net/topic/86274-reporting-issues-useful-information-to-provide/?p=1803748

There Are few special weapons that don't like weapon prifiency, but this does not sound like one, but exact weapon that you Are using could help.