I believe this is documented in Drupal's Form API ReferenceForm API Reference.
Format a set of checkboxes. #options is an associative array, where the key is the #return_value of the checkbox and the value is displayed.
You should be able to set the labels corresponding to each checkbox in the #options array. The array can be of the format:
array(
'submitted_value1' => t('Label 1'),
'submitted_value2' => t('Label 2'),
);
Each key of the array is the value that will be submitted when the form is submitted. The value of each element in the array is what is displayed.