Hey,
You could add -DAFNI_FLOATIZE=YES to the beginning of your 3dANOVA2 command to make it save the output as floats instead of shorts. This should make these warnings disappear. There is a more detailed message about this at the bottom of the help message printed to the screen by 3dANOVA2 if you run it without command line arguments.
Bye,
Colm.