This was due to a bug in SWT or GTK. But the good news is the following fixes the problem
export GDK_NATIVE_WINDOWS=1
To make it permanent you can add this entry into the /etc/environment file or create a eclipse.sh file and add it before calling /path/to/eclipse

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Ubuntu 9.10
- Visitor 2 years 27 weeks ago~/.profile -> export GDK_NATIVE_WINDOWS=1 [failed]
env GDK_NATIVE_WINDOWS=1 /path/to/eclipse [failed]
/etc/environment -> export GDK_NATIVE_WINDOWS=1 [failed]
Gnome unsets this particular variable whenever he can. Is there anyway to forbid gnome unsetting this variable?