I haven't tested the issue in an instance, only in Tol Barad. The map works perfectly fine while in Tol Barad, but reverts back to displaying Atlas when in Orgrimmar.
The following image is when I press "M" to display my map.
And this image, is when I hover the mouse over Carbonite itself, which makes Atlas disappear.
***** Just to add:
Both of the options you mentioned above, were already unchecked. I tried checking both, and alternating between the two, to no avail. Neither of those configurations seem to be the problem.