Without loading these Xara template pages to the sys folder they appear there, is this correct?
Yes, this is correct. The CMS converts any special tags etc. found in page templates to php code and stores the new template file in the sys folder. These end up being the actual files used to display the pages.
I will have spend some time troubleshooting the other issue. If you can provide me with a xar file with the page template that has the issue I'll have a look at it and see if I can figure out what is happening.