Flexicharge doesn't "Suppress" zero value rows correctly

When a charge has the "Suppress this row in the cart if the total charge = 0" checkbox set, Flexicharge does not always suppress the relevant row.

It appears there are two actual problems.

1. The more significant issue is that the code for suppressing the row does not always seems to work.

   For example:

     // hide this charge if required.
  // if (empty($rate) and !empty($misc->hide_if_zero)) {
  if (1) {
    foreach ($txn->misc AS $m) {
      if ($m->chid == $misc->chid) {
        $txn->misc[$m->chid]->seen = TRUE;
        watchdog ('debug', 'Custom3 charge should be hidden...');
      }
    }     
  }
   
   This overrides the test for the rate or the checkbox, so should always suppress the relevant row. But it doesn't. And the log confirms that the code has been executed.

2. The less significant issue is that the test for the checkbox does not always seems to work.

   There are two versions of this test.

   From sitewide.inc: if (empty($rate) and !empty($misc->hide_if_zero)) {
   From shipping.inc: if ($rate === 0 && $misc->hide_if_zero) {

   However, in either case, the latter portion does not always seem to return the expected result (i.e. true if the checkbox is set).

Full example attached.