There are several Samsung and or Google apps that will increase the media server up time and keep your phone awake. I would suggest if you have Currents installed ( I think its there by default) delete any data and cache & disable it. Google Play Music also uses media server - A Lot. Finally you can try turning off 'Samsung Push Service'. I've done this and not had any problems getting emails & messages. Other apps that use the media server are Samsung Hub & Google Now.
Could it be an issue with the ROM you're using? I don't know enough about rooting or hyperdrive to help you there. You can try a Google search for media server and there may be something out there.
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