by Ernesto Rapetti.
Hi all!
I had this very same issue using moodle 1.9 and it turn out that the problem was the max_input_vars PHP limit. Its default value was 1000 and the course I couldn't backup needed more checkboxes to start the backup process.
The solution was to modify /etc/php.ini addling a line like this:
max_input_vars = 10000