I can use the 3 x AA if that will make a difference
I've heard of a couple instances of this now. What I suspect is that the 3.3V logic level from the Flora is too low to reliably register as a '1' with the LEDs operating at a higher voltage. Either the LEDs should be run closer to (or at) the Flora's voltage level, or a logic level shifter should be used on the output.
I am thinking it may just be easier to use the 12MM flat Addressable Leds.
This is with the positive on one side, negative and a wire to (D12) on the other.
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