This message was posted on behalf of Intel Corporation
There is a known issue with the Edison's MCU where there is a delay which affects the GPIOs. If the delay you are reporting is small, then it is the known issue, this is the main reason why a manual PWM might fail using the MCU. We are aware of this issue and we are currently working on fixing it. We hope to solve it in a future software release, nevertheless there is no ETA for a fix.
Thank you Peter for this information.