The first one was the preview version of IntelliJ IDEA 12 which is due to be released next month. I reported the issue on the JetBrains Issue Tracker so hopefully it'll get resolved by the time it's released.
I later decided to use Gimp to create a new wallpaper for my desktop. After maximising the window I found that I was unable to access any of the menu options as the dropdown menus appear behind the application. Thankfully a very good post on askubuntu.com showed a quick workaround for the problem. By adding "env UBUNTU_MENUPROXY=0" to the 'Exec' line in the '.desktop' file you can force an application not to use the global menu.
So in the case of Gimp you would do:
$ sudo vim /usr/share/applications/gimp.desktop
Then edit the 'Exec' line to look something like this:
Exec=env UBUNTU_MENUPROXY=0 gimp-2.6 %U