If a file has been copied to the users root directory, it is not possible to download that file. Instead, you need to create a sub-directory from the users root directory, and move the file into that directory. For example, the file BeebEm9.zip will not download, unless I move it into one of the sub-directories:

The url that AutoIndex generates is:

https://my.fileserver.com/index.php?dir=&file=BeebEm9.zip

If I manually change the url slightly, and add a '/' to the 'dir=' field (so it becomes 'dir=/') then I can download the file.

In the index.php file there is a section of code titled //set the logged in user's home directory:. If I replace that section of code with the original section of code from version 2.2.4 it starts working correctly again, but I'm sure that's not the right thing to do!