A little more information might be required to assist ... from what version of Moodle to what version of Moodle (1.8 to a 2.x, 1.9 to a 1.9, 1.9 to a 2.x, 2.0 to a 2.2.x)? Is it a problem with a single course or all courses?
A suggestion: if single course and on a 1.9, check the course for special roles for the course, roles that have overrides, or roles such as Administrator. In the step for backing up a 1.9.x that shows what roles to include in the backup, un-check them all. If backing up a 1.9 version and restoring to a 2.x, the roles are not included in the restore due to the differences in roles between versions. Then try the restore again.
'spirit of sharing', Ken