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Before entering into a low power state, you have to configure the wake up source you are planning to use. This might be the reason why the microcontroller is not returning to the active state. I recommend you to check the datasheet on page 78 (section 9.2), that section explains the power down sequences: Intel® Quark™ Microcontroller D2000: Datasheet
In page 79 there is a summary of the settings you should do in order to configure a GPIO level triggered interrupt as wake up source.