Yes, Virginia, that’s what Master Pages are intended to do. A background image on the Master Page will appear on all instance pages. If you change the Master Page the instances pages will update after you republish with affecting any other items.
Okay, I figured out what the problem is. For whatever reason I didn’t use the page wrapper from the master page and instead opted to add my own for the first web page, which also affected all the pages, which were duplicates of the first.
Can I simply add a new page wrapper to the master and then drop all of the inline boxes into that wrapper?
To achieve the backgrounds for page and window you don’t necessarily need a ‘wrapper’, which sounds like you are using the old method of coloring an item and sending it to the back. Make sure you select background colors from the Inspector - this way you don’t need a ‘wrapper’ item. To do this make sure nothing is elected on the page, go to the Inspector palette, and click on the pen icon.
Do this first for the Master Page. Then, do not create new pages by duplicating the first one. Create new pages from the Master, either from the menu: Page/New Pages, or in the site panel on the left by dragging the Master into the area below.
You then don’t need a wrapper - you can simply place items on the page - or group them if you wish.