Currently the [All Configurations] selection for the build configuration (introduced with CDT 5.0 / Ganymede) does not work as expected for AVR properties (it is basically ignored).
With CDT 5.0.2 (expected in February 2009) the Plugin will throw a java.lang.ClassCastExceptions when [All Configurations] is selected when on one of the AVR property pages.
The AVR Eclipse Plugin needs to be made aware of the MultiResources used by CDT 5.0.