William,
I am still in the beginning stages of the investigation, but it looks like perhaps some of the graphics (the ones that are the correct size) were imported from a project that was built as 1920x1080 and imported into your project that was 1280x720; and then others were built native as 720p. Can you give us more info on the history of these scenes and if indeed they were imported between projects of different resolutions?
I notice that if I create a new quad in the "broken" scene and set it to exactly 1280x720 then it fits the screen perfectly. If you do the same in the "Good" scenes, the 1280x720 quad is actually smaller than the scene.. Leading me to realize that the "good" scene is actually the one behaving strangely (and I believe must have been created originally with a 1920x1080 raster)
#XPression