Hi Mark,
The problem is being caused because the script is not picking up links that are contained within javascript menus. This would be the same for search engine robots too.
We have created a search engine robots simulator on the site at
http://www.xml-sitemaps.com/se-bot-simulator.html Here you will see what links they will pick up. The 2 pages you previously mentioned are no problem as you have direct links to them from your home page.
Although the remaining pages can be picked up from
http://www.shipwreckcoastaccommodation.com.au/port-fairy-accommodation/port_fairy_cottages.html this page is an orphaned page as there are no links to it that are readable to search engine spiders.