Not sure how to reproduce this, but if in the main workspace I load only 2 tabs with panes inside, one of the two tabs will work properly (usually the first loaded one), but the other tab with panes inside won't be recognized by the rest of the interface. looses shortcut ability, context menus, etc.
Quick screenshots.
First tab with panes behaves normally. Focus is in grid and the main toolbar (File, Edit, ...) appears normally.
Second one doesn't. Focus is in in grid, but the main toolbar at the top (File, edit, View, Tools) appear as if the focus isn't in a grid, or if IQ had just loaded, with no grids.