Dynamic Form Field Submit Handler
Well after ignoring this problem for a while it was time to find an answer.

The issue was with using $form['#tree'] = TRUE; 
I didn't use the full array references after that...eg:
$form_state[$i]['description'] needed to be
$form_state['values']['items_fieldset'][$i]['description'] = 'foo';
(

After that I just used a foreach to grab my values from the dynamic field values...like:
foreach ($form_state['values']['items_fieldset'] as $v){
$submission->description[] = $v['description'];
}

And last was to dump them into my DB, and life is good.