How to add inline Javascript code properly with drupal_add_js for a Drupal Commerce checkout pane?
Presumably you're using hook_commerce_checkout_pane_info

Try using $form['#attached'] to add your js to the checkout pane form instead. That may work better there.

$form['#attached']['js'] = array(
  drupal_get_path('module', 'my_module') . '/checkout_pane.js',
);