When is the HTML5 overlay for the MediaLive channel inserted? Is it done before the channel has started? After the channel has begun? You may want to test starting the insertion after the channel has been started. Motion Graphics overlays needs to be enabled in the channel, then insertion turned on/off via the Scheduling function.
Dynamically changing the resolution in the MediaLive RTMP input may cause other issues. Creating a 720p output from lower resolutions will yield a poor quality image. Have you considered varying the bit rate of the RTMP signal and holding the resolution static, if possible?
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