In some repos in our local phabricator installation, Diffusion does not list all folders. When the URL is manually set to a folder which was not listed however, its contents are displayed correctly. We run the current stable version of phabricator, the problem persists even after rebooting the server.
The first image shows the browsing view of the repo root in the default branch, note that there is no src folder listed.
when /src is added to the url, the contents of the folder are displayed correctly.