On my first character I'm missing 2 items from the Valuables collection and 1 item from the Odds and Ends collection. She has found all of the items from the other, later, collections.
There may be some items you can only find in certain locations, and I'm thinking it's because I never used Port Royal caves for anything with that or my test character. I just always used Tortuga because I knew where to find what I was looking for there. It has only been since playing my second open character that I have learned where things are on Port Royal, and the wonders of Murky Hollow... and how often I can find myself landing on my tush while playing around in there.
