I can confirm this on Ubuntu 9.10. I can also confirm this bug when running /usr/lib/eclipse/eclipse directly without the /usr/bin/eclipse wrapper script that sets GDK_NATIVE_WINDOWS=true, among other things.
It looks like what is going on here is that when you open a java file, the editor is not stealing focus from the package explorer, so it is not surprising that CTRL-F searches in the package explorer instead. If you start typing, you get the search box in the package explorer as well.
I can confirm this on Ubuntu 9.10. I can also confirm this bug when running /usr/lib/ eclipse/ eclipse directly without the /usr/bin/eclipse wrapper script that sets GDK_NATIVE_ WINDOWS= true, among other things.
It looks like what is going on here is that when you open a java file, the editor is not stealing focus from the package explorer, so it is not surprising that CTRL-F searches in the package explorer instead. If you start typing, you get the search box in the package explorer as well.