Right, that's what's supposed to happen.  As per the spec, 
browsers don't send checkboxes in the request if they 
weren't selected.

This is a browser issue - try this sample code:

<form>
<input type="checkbox" name="test" />
<input type="submit" />
</form>

Note how when the checkbox is not selected and submit is pressed, the query string consists of only '?'

If you need to keep track of what checkboxes are on a page, you could set a list in a hidden field and then use PHP to compare the list of fields in the hidden field to the fields passed to the form.

Something like this:

<input type="hidden" name="checkboxes" value="foo,bar" />

<?php
foreach (explode (',', $checkboxes) as $field) {
   if (isset ($$field))
       continue;
   $$field = 0;
}

?>