Hi, Cyclosaurus,
I'm an old holdout on iWeb, still using it in November 2013. Since the Mavericks upgrade (I'm pretty sure that's when my problem started), after I publish, save, and quit, when I open iWeb up again, all the pages are red (on the leftside menu of pages), as if they're all changed and unpublished, even though neither is true. That's fine, but then when I make changes in iWeb and go to "Publish Site Changes," iWeb connects with my web hosting service and then gives me this message: "A folder with the name "Site" [this is my website's name in iWeb] already exists on the server. Do you want to replace it? Replacing it will completely overwrite the current contents of the folder on the server." Then I have the options of "replace" and "cancel." When I click "replace," iWeb uploads my entire website to the server again, and not just the parts that are changed. It's like, somehow, my web hosting service is making no connection to me as it used to. That is, it's treating me and my new content like it's all brand new and foreign. This is problematic because I have lots of video and audio content on my site, so the publishing of the whole site takes hours and hours. Once it's published, all's well online with my site, but how do I get iWeb to not republish the whole site again?
Maybe my site structure is broken, like you mentioned above. If that's so, how do I fix the site structure? Thanks!