Hi,
The version 1.1.9 is ONLY for the Phantom 3, the controller will remain on the previous version 1.1.8 and does not need updating ( strange and confusing yeah, I know ).
As for the controller not controlling - After the Phantom's update to 1.1.9 you might well need to pair the craft and controller again ( I know you said it seems done but give it a go ).. Follow the image below or see page 28(ish) if the manual.
Remember to buy extra propellers and one or two spare batteries to keep you flying
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