OK, couple things worth mentioning:
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For flashing over USB, make sure you plug your micro USB cable into the Daisy Seed itself, and not into the secondary USB port on the Pod.
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There are two red LEDs on the Daisy Seed, one on each side of the micro USB port. The one that is labeled USER should be flashing periodically when you receive it. The other LED labeled PWR should be illuminated whenever the Daisy Seed is powered.