There are many context toolbars in Atlantis: the "Table" toolbar, the "Header & Footer" toolbar, the "Footnote" toolbar, etc. They display only under certain conditions. You can disable individual context toolbars through the toolbar customization dialog. But note that you would be unable to access the features offered by the disabled toolbars.
Thanks very much for your help -- and for anyone else who encounters this -- I did find that if I pulled the Right boundary marker back to the Left -- adjusting the toolbar to make it narrower -- this was a main fix.
Then the other thing I noticed, was that the "context toolbar?" which kept "taking over", was the Hyperlinks toolset --
because whenever I would change documents, to a document without any hyperlinks in it, the Hyperlinks "context toolbar" would disappear from the top,
but then when I clicked back on a document that included some hyperlinks, that toolbar would reappear.
But as you suggested, in the beginning I had my "Custom 1" toolbar too wide, too full -- such that when the "context toolbar" was activated, it would force my Custom 1 toolbar 'off the screen'.
Atlantis might display multiple context toolbars simultaneously. For example, if you select a picture in a table located within a document header, there would be at least three context toolbars displaying: "Header & Footer", "Table", and "Picture".
If you need context toolbars (the most typical scenario), but do not want to do toolbar scrolling, leave a sufficient amount of free space of the toolbar area for at least 2 or 3 context toolbars. You can also resize context toolbars (make them narrower) through the toolbar customization dialog.
If you do not need context toolbars, you can disable them through the toolbar customization dialog.