Can't write to known_hosts
Given that the file has extended attributes and on a fresh install doesn't I'd start by removing them, xattr -c ~/.ssh/known_hosts. 

When you say you can't write to the file, do you mean directly or via ssh adding a host? I'd try cat ~/.ssh/known_hosts to make sure you can open it. Then you might try cp ~/.ssh/known_hosts ~/Documents/known_hosts and echo "Delete this line" &gt;&gt; ~/.ssh/known_hosts to see how that goes.