With latest graphene version (1.9.4.2), the total size was increased from the default 960px to 1100px, while opting for the 2-column mode display (with the widgets sidebar).
Doing so, no mather which size is selected for the 2 columns, the widgets sidebar is not matching anymore and is displayed below the first column anytime.
Only reverting back to 960px total size is correctly again showing the 2 columns.