Not sure if it's the addon but when I disable it all my items show up, when i have bagnon active for example none of my flasks show in my bag or my hearthstone and random pieces of gear however they are still there because I can use flasks on my bars, cast my hearthstone using /use hearthstone and equip gear with the gear outfitter.

Check the FAQ

I've always had bagbrother installed... linking a screenshot of what I mean.

As you can see, I have all addons installed and loaded, my hearthstone isn't showing in my bag, but it's in there because I can /use hearthstone.

Check the FAQ: bags are hidden