Right, I have managed to work around a majority of the problems that I have, but one of them comes from the change in the way the extension for Data Assist works now in comparison to how it used to before it was bundled into Data Bridge.
The PowerCMS Builder creates a template and the previous version of Data Assist required a template in which to add the content it produced. The template from PowerCMS has a number of php requires and other php code above the head tag. When I apply the template to the page, this code is deleted and replaced by the php code created by the template-less Data Assist page... this is where a number of my issues came from! Security Assist I have side stepped and simply entered the code by hand on each page that needs protecting, and now they work fine.
I am still getting this 404 not found URL error from pages that I have used Data Assist to Insert new or update pages even when I have commented out:
//if (function_exists("rel2abs")) $WA_redirectURL = $WA_redirectURL?rel2abs($WA_redirectURL,dirname(__ FILE__)):"";