What you need to do is buddy is take your SD-Card out in the side of your 3DS and your GW card of course and format your systemnand in settings and set up your 3DS again as normal, this will separate your both nands from each other and you wont find that issue happening again and also no internet settings will set up in systemnand when you set them up in Emunand, nothing will copy itself again in systemnand, its a great method and good little handy trick to use!. I had the same happen to me but that sorted it out for good and is well worth doing for other little annoying things in systemnand that happens! Trust me on this m8, go and do it!
Edit: Just remember when you have formatted a fresh systemnand you need to run the blue GW card to set up the exploit again for gateway to work but that's no hassle.