With the default max_input_vars setting of 1000, large backups (i.e. those containing lots of activities and/or resources) can't be restored in their entirety. Although the full array of checkboxes are displayed on the "schema" page, the "review" page will only show them ticked up to a certain point, at which everything else is shown with a cross. This is because max_input_vars has been hit - and is probably easiest to replicate by lowering your max_input_vars setting and using a backup of the features demo course - unless you happen to have a backup handy that has vast numbers of activities and/or resources (the features demo course does not contain enough to encounter this at the default of max_input_vars=1000).

The solution is to refactor the form so that it uses arrays of fields, as max_input_vars applies to each level in an array (i.e. you can have at most max_input_vars top-level fields, but each of those can be an array containing up to max_input_vars elements, each of which can also be an array up to max_input_nesting_level (default 64) levels deep). See MDL-35074 for an example of doing this in the gradebook, though it may need to be dealt with slightly differently if the restore process does not use data_submitted() to retrieve all fields in one go.