The reason for the behavior you are seeing is that @predefined contains an array reference, rather than a plain value. Since you don't show how you defined @predefined, it is impossible to say where you went wrong. Suffice it to say that:

print
  $q->checkbox_group
  (
    -name=>'predefined',
    -linebreak=>'true',
    -values=>@predefined,
    -defaults=>param('predefined'),
  );
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is not the right way to pass values to a CGI method. @predefined will be flattened into the argument list. If @predefined contains a single value, you've lucked out and it will work okay. If @predefined contains an odd number of values, the first will be taken as the value for the -values key, and the rest will be taken as separate key/value pairs. Worst case, if @predefined contains an even number of values, all the remaining explicit key/value pairs will be shifted by one, so that the keys are used as values and vice versa.