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If you – as one(!) example – select all (cmd+A) and look at the left side of your A-Master, you’ll find tons of 3rd party widget elements (QooQee, Animated Transitions; MuseResource, MLOVE, …).
If you delete them all, miracles happen and your footer suddenly is placed, where it has to be placed.
In other words: These widgets cause the problems.
Annotation 1: You know, that all visible elements outside the page/breakpoint width cause mis-displaying on mobile devices? (These devices try to display all content of your page/breakpoint and therefore have to heavily zoom out the content.
Annotation 2: I think, it is not a very good practice to let potential helpers download a 700 MB(!) .muse file only to enable them to second. Why not reducing the site to one page with only some objects? This would delight the helpers and has an important side effect: If you had done this, you certainly would have recognised the "bad behaving" elements by yourself.
Got you, I am new to all of this, I am not familiar with sending download links. This was my first time doing it. I will take that in consideration for next time. I was under the assumption that the 3rd party widget elements could be placed anywhere and would disrupt the functionality of the site.
The main problem seems to be, that these widgets aren’t fully Muse compatible.
Try it by creating a new site with your footer items, place the 3rd party widgets one by one and you’ll see …