Did you see that when you make a forwader, you get two files right? one is .cia, and other .nds, each one has like 1.30 mb size.
As you said, keep the cia in cia folder, and you don´t need the other one .nds created by the forwader.
Everything is fine, but, in Nintendo Ds room folder, you must put the .nds game (is like 128mb size), and not the .nds forwader that u get doing the app process.
As in the picture above, you don´t need the file selected (in blue), yo just need the cia file... don´t even touch the other one cause u don´t need it for nothing.