So you out the original .nes rom in the same folder as the .3dn file both with the same name but different extention and open the .nes and it should launch? Its not working for me if this is correct.
oops 1 year late sorry but to those having trouble launching a game make sure that it's vanilla US copy not hacked or other regions etc. that's how I solved my launching issues. find a diff version of the rom until one works. yes same name and same directory as the .3dn file