Be careful with that, flag1 does NOT use a number, so it's just "flag". Only the second and third flags use a number.

In fact I suggest you to NOT to use more than one flag per assertspecial as they will have 1 tick of delay per order (So the first flag will be instantly activated but the second and third will do it a tick or two later).

Instead just divide the assertspecials into two different sctrls like this:

[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = nomusic
[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = nobardisplay

[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = noBG

[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = nobardisplay

[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = roundnotover

[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = nomusic

[State -3, Message]
type = Explod
trigger1 = matchover && !alive && Time = 120
anim = 1
ID = 1111
pos = 160,60
postype = left
facing = 1
removetime = -1
scale = 0.25,0.25
ontop = 1

Use this assertspecial to stop the fade to black:

[State 0, AssertSpecial]
type = AssertSpecial
trigger1 = whatever you want
flag = roundnotover

And your music doesn't stop because you forgot to add a "2" here:

[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = nobardisplay ;works
flag2 = nomusic ;doesn't work

;--------------------------------
; MESSAGE AFTER DEAD
;--------------------------------

[State -3, AssertSpecial]
type = AssertSpecial
trigger1 = matchover && !alive
flag = nobardisplay ;works
flag = nomusic ;doesn't work

[State -3, Message]
type = Explod
trigger1 = matchover && !alive && Time = 100
anim = 1
ID = 1111
pos = 0,0 ;Provisional
postype = p1
facing = facing
removetime = -2
scale = 0.25,0.25
ontop = 1

Mugen.cfg, [Debug] section, set Debug, AllowDebugMode and AllowDebugKeys to 0.

Mugen.CFG

Should be in the root of folder ""Data"".

[Options]
; Basic options
Difficulty = 6
Life = 100
Time = 99
GameSpeed = 0

No, you can't limit continues.

Code:

[State -3, Voice]
type = PlaySnd
trigger1 = numExplod(6000) > 0
volumescale = 300
value = F900,var(3)
channel = -1
persistent = 0
loop = 0
ignorehitpause = 1

That would be your culprit. Also, to note, persistency won't work in State -2 or -3 due to the nature of those states. Try this:

Code:

triggerall =  NumExplod(6000)
trigger1 = var(#) := 1
trigger1 = !var(#)

Then reset var(#) to 0 sometime in the near future.

[State -3, Voice]
type = PlaySnd
triggerall =  NumExplod(6000)
trigger1 = !var(4)
trigger1 = var(4) := 1
volumescale = 300
value = F900,var(3)
channel = 0
persistent = 0
loop = 0
ignorehitpause = 1

[State 0, VarSet]
type = VarSet
trigger1 = !NumExplod(6000)
v = 4
value = 0

[State -3, EXPLOD]
type = Explod
triggerall = numExplod(6000) < 1
//Other triggers to trigger the explod
ID = 6000
anim = F600
//position and these stuff
ontop = 1
ignorehitpause = 1
persistent = 0

[State -3, Choose a voice]
type = VarRandom
trigger1 = numExplod(6000) > 0
v = 3
range = 0,8  //There are 9 sounds, from 900,0 to 900,8
ignorehitpause = 1

[State -3, Voice]
type = PlaySnd
trigger1 = numExplod(6000) > 0
volumescale = 300
value = F900,var(3)
channel = -1
persistent = 0
loop = 0
ignorehitpause = 1

Using layerno = 1 will put a stage element in the foreground. This will bypass any sprpriority. However any explod using the parameter ontop = 1 will draw over the top of this and you cannot prevent that short of using ontop = 1 much less.

p1.bg0.layerno = 1
p1.bg1.layerno = 1
p1.front.layerno = 1
p1.counter.layerno = 1

Here.