Problems with $_GET variables

This was previously working, but since re-installing wordpress it is now no longer working. My script has a pagination system that relies on the $_GET['page'] variable. However, wordpress is dropping the variable at the end of the url, so instead of http://proof.chillifish.com/dcc/all-cottages/?page=2 It's changing it to http://proof.chillifish.com/dcc/all-cottages/2/.