What version of Wowza Streaming Engine are you seeing this with? If not already on 4.5.0.01, and you have active Maintenance and Support please test this with Wowza Streaming Engine 4.5.0.01.
If this is still occurring after updating to 4.5.0.01 then please consider opening a support ticket with us. Include a zip of your /conf /logs /transcoder and /manager and we can take a closer look for you.
What version of Wowza Streaming Engine are you seeing this with? If not already on 4.5.0.01, and you have active Maintenance and Support please test this with Wowza Streaming Engine 4.5.0.01.