When I have 6 pieces equipped in my APC it still shows 'gather extra resources' as inactive, why?

Are all of your pieces blue level or above? That is the requirement 4 blue or above for faster gathering, 6 blue or above for extra resources.

If you do have this then it may be a bug, try removing them and putting them on a different APC perhaps. If this doesn't help then try reporting it to the developers in the in game support system.