Depending on what you're doing with your Ouya it could be making new copies everytime you boot for some reason. Deleting your init.d scripts /shouldn't/ mess anything up but I don't suggest deleting them as they do all the kernal tweaking and it will go back to stock. Make a new folder called init old and put all the files here. That should put your system to stock and then next time you start up a new init file will be created in it's place. They shouldn't be interfering with anything but give it a try.