Backup fails when Moodle is at WWW root, not in folder

We are unable to backup and restore a course where the contents of the moodle folder have been installed in the www root directory, and are not in the usual moodle folder. (We do this so the moodle opens at the URL mydomain.com, instead of mydomain.com/moodle. It works.)

Backup goes through the motions, but restoring it to a different server results in a blank page, sometimes with a "course" called something like "restore in progress."

Anybody succeeded with this? Any clues how to fix it?

Thanks.

Running Moodle 2.5.5 on an ample server, with accentuate theme.