by John Hackett.
Not sure if this is still an issue with people but just in case...
We had the same problem (v 2.6.1) and found that there is a settings in the admin panel to control the "import_max_general" value which defaults to 10.
In "Site Administration" -> Courses -> Backups -> General Import defaults
Change to a number larger that the total number of courses in the installation - we used 1000 which fixed the issue.
John.