Are you sure the FPS counter is working well ? I have done those tests yesterday :
A- DS lite, downgrade the sound to reach 50FPS, game : Burger time
B- N3DS with TWL++ in DSI mode for extra CPU power, default sound option, 60 FPS, game : Burger time
C- N3DS, Retroarch FreeIntv, standard options, 60 FPS, Burger time
What I have noticed :
1) In terms of game speed, A and B are very similar when they are side by side, if the sound was not downgraded it would be difficult to see the difference
2) Even if in DSi mode 60FPS, FreeInt is faster and smoother at the same framerate, it is running at the "true" speed.The guy in Burger Time is moving really faster.
3) Nintellivision has got washed out colours compared to FreeIntv
I will check this again tonight after work to be sure that I did not miss something, mainly with the frameskip option.