I think it depends on if you are a second user perhaps.
I created another user for a friend, to store some files, but when they logged in they couldn’t see anything.
So I had to user Domains->Re-map Sub dir to change where the direction went.
For example, if I wanted user1 to be the main one, but user2 is to manage images at www.domain.com/images, I would set up a remap to /home/user2/domain.com from www.domain.com/image. Maybe this is your problem?