When adding a new page to a project, all pages are flagged as changed even if that page is set to "not shown in navigation". The reason for this is because when you add a new page it automatically gets added to the website navigation, this in turn means all pages would need to be updated to reflect this new page.
However, even if you switch the page to "not shown in navigation", RapidWeaver still belives there are some chnages to be publshed. This is due to the fact that RapidWeaver doesn't keep a history of each change made.
The good news is that even if all pages are marked as changed it shouldn't take too long to publish as RapidWeaver knows that none of the images have changed so will only upload the HTML/CSS files.
We hope to improve this feature in future versions of RapidWeaver.