FPS limiter isn't working I'm afraid (tried toggling it on & off in the menu), Ms Pacman is getting 86/87fps for the PAL rom and 93/94fps for the NTSC rom. n3ds obviously.
BTW was probably just a typo in your post, but NTSC is 60fps and PAL is 50, not vice versa.
Perusing the code, you do have the 50 and 60 the wrong way around. Also is the FPSLimit flag meant to be declared as a double double (dd)? It's initialised to 1, but also it's toggled with FPSLimit = !FPSLimit; - does that work with a numerical value?
EDIT:
Made a few tweaks. Haven't learned pull requests yet sorry, guess I should do that next. Now the framerate is actually being limited, but it seems it's not quite right, reported fps is more like 67 for ntsc or 59/60 for pal.
I changed the FPSLimit variable to an int, changed its toggle code to 1 - FPSLimit, and in srv_Flip in flip.c you don't need to divide Ticks_per_Frame by 1000. I also tried changing hidKeysHeld to hidKeysDown in gui.c, but you can probably ignore that as it didn't seem to make much difference.