Hello!
I had annoying problem when Studio is opened in “child” window: the top menu items were under Module Studio layout (root div is #mdlayout). Similar bug was when small portion of text were running under the header menu (when the output is small).
Here is my solution:
insert into style.css (found in /themes/Suite7/css/style.css) following CSS definition:
#header {
float:none;
clear:both;
z-index:100;
}
now the header menu will always be on top and having nothing under it.
I hope this helps.