This is a weird one.
My markup is rather large so I'll just include a collapsed summary of my windows. The full declarations can be found at the end of this thread.
All of the windows use ContentTemplate.
The issue is that "one" of these windows will display the footer from the master page.
If I re-order the windows, then the footer appears on another one.
It appeared that whatever window was in the 3rd position (winAutoSave in the snippet above), would have the footer - but I've found that is not always the case.
Another important clue is that this only occurs in Chrome; Firefox and IE are fine and do not show the footer on any of the windows.
I have attached a file containing a screenshot showing the issue on the Auto Save popup.
The fact that merely changing the sequence in which the windows occur in my page makes me believe that it's not a problem at my end.
Here's the full markup for the windows - the footer and referenced class from the master appear at the bottom: