When we click the softaculous button, it replaces parent (not a pop-up but a window replace) and we lose the cpanel mast etc. and SA is in the browser all by itself!
When we click go back to cpanel, it does indeed, replace the entire window with cpanel, as you'd expect.
We DO have this "ticked"
Show Softaculous in cPanel's Native UI.
If this is enabled then Softaculous will be shown in cPanel's Native UI.
I appreciate this may be a theme issue, but this seemed the place to ask in regards to SA integration ;-)