Details
Description
Currently there is a z-index conflict with #civicrm-menu and modal (ui-dialog) windows.
Example, when a modal opens and the user has a short window, a portion of the modal window is hidden by the #civicrm-menu.
Recommendation for your review:
Change z-index of #civicrm-menu to 800 instead of 9000. Still greater than the toolbar but less than the modal.
#civicrm-menu
However; if there's a good reason to keep the z-indexing at 9000 then perhaps the .ui-dialog z-index change be changed from 1002 to 9999 so it's always on top.
CSS Overview
Here are the layers with z-indexing as they exist now:
#toolbar
/(toolbar.css line 34)/
#civicrm-menu
/(menu.css line 66)/
.ui-dialog
/(created on the fly)/
So .ui-dialog windows appear over the top of the toolbar but under the civicrm menu.
I've attached a patch with this change to /sites/all/modules/civicrm/packages/jquery/css/menu.css.