Well, the scripts uploaded by the XDK should be stored in the Edison and run every time you boot your board. If this is not the case, then probably you need to check the XDK daemon or the XDK IDE version. They may be out of date and could be causing this issue. Also, are you using the latest Yocto image? If you're not, then you can get it in Intel® Edison Board Download | Intel® Developer Zone. This may also help you fix some issues.