make sure your mugen.cfg goes to the system.def you want it to.

make sure you added your intro to the system def like my MKintro.def(currently working on)
[Files]
spr = data/system.sff ;Filename of sprite data
snd = data/system.snd ;Filename of sound data
logo.storyboard = ;Logo storyboard definition (optional)
intro.storyboard = MKintro.def ;Intro storyboard definition (optional)
select = data/select.def ;Character and stage selection list
fight = data/fight.def ;Fight definition filename
font1 = font/f-4x6.fnt ;System fonts
font2 = font/f-6x9.fnt ;System fonts
font3 = font/jg.fnt ;System fonts
make sure its next to intro.storyboard =

now make an intro.sff file.add all those good sprites.

now add this to your first line in intro.def
[SceneDef]
spr = (filenamehere).sff
startscene = 0
[Scene 0]
fadein.time = 120
fadeout.time = 30
bg.name = BG0
end.time = 6115;(this is pretty much like an time limit)

[BG0Def]

[BG0 (your title here)]
type = anim
actionno = 0
start = -160, 0;(if the images are in 320x240 use this preset)
layerno = 0

[Begin Action 0]
0(group #),0(image #),0(X axis),0(Y axis),2(time for every frame)

and thats pretty much it..basic...