Hi Luke,
I don't have an Apgoee, so I can't confirm that it works, but there should be nothing special necessary to enable the servo outputs (you can explicitly disable them by setting USE_PWMx to 0 though).
So I guess some of your gpio pins are dead...
I wrote a small gpio test prog for something similar a while a go (added it to master now), you could use it to test the gpio output:
<firmware name="test_progs">
<target name="test_gpio">
<define name="TEST_GPIO1" value="GPIOA,GPIO2"/>
<define name="TEST_GPIO2" value="GPIOB,GPIO4"/>
</target>
</firmware>
That will toggle the gpios with 1 and 2Hz respectively.
Cheers, Felix