Included a test case to reproduce the issue:
"Preferences" action is in "Edit" menu, but gets (as expected) repositioned by Qt to the application menu
1 - Launch the application and see the 3 menus in the menu bar "test", "Edit" and "Menu2"
2 - Click on the first button "Open Modeless Dialog" to see how opening the modeless dialog disables "Preferences" on the main menu and "Edit" and "Menu2"
3 - Click ok to close "test modeless dialog"
4 - Note the menu options are enabled again but Preferences is not

This was working with Qt 4.6.3 and the problem arises after commit:
0e6abffa2843bae594195b9ba56d5c5264837288

Included a patch to work around this issue