You appear to have a either a closure or global variables on $query, $file, and %list. Under various conditions you may get unexpected results. It is better practice to pass values to subroutines as arguments.

sub printboxes {
    my ($query, $file, %list) = @_;
# ...
    open FH, '> ' . $file or die $!;
    $query->save(FH) or die $!;
    close FH or die $!;
}
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I added some error checking on the save operations, so you get better information if something there is the problem.

Update: The data you get saved suggests that $query does not have any data in it. Could be the kind of unexpected behavior I mentioned. Or do your test runs neglect to provide data?

After Compline,
Zaxo