When using any java application in gnome-shell if the window is maximised the pointer position is way off; but only on the menu's, in the editor, or the side panel, the pointer is fine.

This only presents itself when the window is maximized, and it seems that the further away from 0x0 the window is when you maximise it, the bigger the pointer offset.

From what I have gathered it has to do with the window not updating it's size when it gets maximised.

The other issue is that when a gnome-shell notification appears, when clicking on it, I lose the ability to type in the editor, I can select text etc, but can't give it focus to type. I must bring up some other text input (e.g. right click on a file on the left, select rename, which brings up a rename dialog) after that I can type in the editor again.

So, how can I fix this?

Below is as much information as I can think to provide

$ gnome-shell --version
GNOME Shell 3.6.1

$ java -version
java version "1.7.0_09" Java(TM) SE Runtime
Environment (build 1.7.0_09-b05) Java HotSpot(TM) 64-Bit Server VM
(build 23.5-b02, mixed mode)

$ file /etc/alternatives/java /etc/alternatives/javac
/etc/alternatives/java: symbolic link to '/usr/lib/jvm/java-7-oracle/jre/bin/java'
/etc/alternatives/javac: symbolic link to '/usr/lib/jvm/java-7-oracle/bin/javac'