Mike,
The Comment module in JFBConnect is triggered off the URL of the current page. I'm not sure what the URL the other code was generating and using, but we'd need to know that to understand where the difference is.
I just tried viewing the following page:
/jobs/ad/farm-factory,288/8-100,497
In the code is the following for the comment box:
<div class="fb-comments" data-href="http://www.plipli.com.au/jobs/ad/farm-factory,288/8-100,497" data-width="auto" data-mobile="false">
That matches the current URL, which is what I'd expect. If the old comments were attributed to a different URL, then they wouldn't display on the current page. That's expected. In that case, you'd need to specifically add the JFBCComments module on each page with the 'other' URL as the target since the previous comments were attributed to some other URL.
I hope that helps explain, but if you have any questions, just let me know.
Thanks,
Alex