that's the problem - you have explained them on a logical level - and he understands them on that level - but it isn't dealing with how they make him feel.
Obviously something has happened to frighten him - you might eventually find out what - but in the meantime you have to work out with his help exactly what it is the bothers him and why that is extending to other things.
Try by saying something like - I can see you are worried by pine cones. (sit him on your lap and have a cuddle conversation so that he feels really safe). Say you want to help him avoid the problem (to start with, later you can tackle overcoming it), and say you need him to explain what it is about them and what they make him feel like. Then talk through with him ways of getting round it - maybe write down all your ideas (his and yours - godd and silly ones), then go through them all and decide between you which ones are worth trying. Throw some silly ones in too - like maybe taking a mini hoover and hoovering them all up, or walking past them with your eyes closed.
That way he feels a) that you are really listening to what he is saying, and b) that he is helping to solve the problem for himself.