If a broken symlink exists in the folder, it will sometimes prevent other files and folders from being listed in the Browse Files page.

To reproduce:
1. Create a new site
2. View Browse files page
3. Create a broken symlink in /files
4. Refresh, and some files might disappear

It doesn't occur every time and I can't think of how to narrow it down further. Hopefully you will see it occur when you try the above steps.