displaytoclipboard or appendtoclipboard.
http://www.elecbyte.com/mugendocs/sctrls.html#displaytoclipboard

[mcode]
type = DisplayToClipboard
trigger1 = 1
text="var(17) = %d"
params = var(17)
persistent = 0 
ignorehitpause = 1
[/mcode]

This will show the value of var 17 at all times on the debug text portion of the screen.

;Example 1
[Command]
name = "Normal"
command = ~D, DF, F, y

[Command]
name = "Super"
command = ~D, DF, F, D, DF, F, y
time = 30

;Example 2
[Command]
name = "Normal"
command = ~D, DF, F, y
time = 10

[Command]
name = "Super"
command = ~D, DF, F, D, DF, F, y
time = 30

;Example 3
[Command]
name = "Normal"
command = ~D, DF, F, y
time = 10

[Command]
name = "Super"
command = ~D, DF, F, D, DF, F, ~y
time = 30

;Example 3
[Command]
name = "Normal"
command = ~D, DF, F, y

[Command]
name = "Super"
command = ~D, DF, F, D, DF, F, ~y
time = 30

The ! is at the wrong spot.
It's !enemynear,Ishelper.

However :
-You are supposed to use target,Ishelper instead. It doesn't matter what the nearest enemy is (helpers are not enemies, anyway), if what you are hitting is not the nearest enemy. What matters is the player you hit, and you check that with the target redirection.
-You might hit more than one target (either in simul or if the opponent has cloning abilities). In this case, you can at most check one of them for being a helper or not. So you should either make it always or never change if there is more than one target, or you should make the attack unable to hit more than one target.
-You might have zero targets. (if the move hits a hitoverride) To avoid debug spam, you need to make sure there is at least one target in a triggerall line.

I'd suggest using this for the change condition :

Trigger1=(Movehite=1) && (numtarget>0)

Why? Because hitting projectiles or anything that has a hitoverride active doesn't become a target. So if you have a target you either managed to hit a player or a player clone, as non-clone helpers always need to use hitoverride.
Also, if the thing you hit did have an active hitoverride, then it's impossible to tell if it's a helper or a player.

[State 0, ChangeState]
type = ChangeState
trigger1 = movehit && enemynear,!IsHelper
value = 2925
ctrl = 0

[Info]
name = "naruto"
displayname = "Naruto"
versiondate = 2011
mugenversion = 1.0
author = "jjmugen"
pal.defaults = 1

[Files]
sprite = naruto.sff
anim = naruto.air
sound = naruto.snd
cmd = naruto.cmd
cns = naruto.cns
stcommon = common1.cns
st = naruto.cns
pal1 = naruto1.act
pal2 = naruto2.act
pal3 = narutoS1.act

[Arcade]
intro.storyboard = intro.def
ending.storyboard = ending.def

[Palette Keymap]
x = 1  ;Press punch for pallete 1
y = 1
z = 1
a = 2 ;Press Kick for pallete 2
b = 2
c = 2
x2 = 3 ;Press Start + punch or kick for pallete 3
y2 = 3
z2 = 3
a2 = 3
b2 = 3
c2 = 3

You're in luck. I have a 1280x1024 monitor and found your solution.

Your graphics card is resizing the screen to stretch, it's not a MUGEN problem.

(I'll be roughly translating here, since my system is in Spanish)
If you have NVIDIA then go to the NVIDIA Control Panel->Screen->Adjust Desktop's size and screen position, under there change: Make scale adjust from Screen to GPU.

Attaching a screen so you can guide yourself:


I dunno how you do it in ATI cards.

Sprites disappear but leave a shadow if you have a time = 0 frame in the animation. This mostly became a problem with fighter factory and it's penchant for setting the time for frames to 0 by default rather than 1.

Basically if your turn sprites have a frame time of 0 anywhere, they'll vanish and leave a shadow.

This should also happen if you jump over your own character though?

Doublecheck the guard states to make sure none of them have 0 frame times as well.

This is what's happening :

The AI is guarding (state 131).
There is no AI code in state 131 to tell it to keep guarding, so it stops guarding at random and goes to standing (state 0).
The opponent is on the other side, so it plays the turning animation (anim 5).
Then it goes to the walking state (but is still playing the turning animation)
Then the AI makes it guard again, but it stops the guarding immediately, so it ends up in the guard end state (140).

The problem is pretty much that anim 5 (turning) is probably missing or uses a non-existing sprite.
The shadow staying there sounds strange, though. Maybe the turning sprite is misaligned so it appears below/above the visible area.

Did you try playing on the other side (P2 if you normally play as P1)? Maybe the bug is related to player sides and not to who is playing it.

Do you have any turn related code in your minus states that activate while guarding? Or any other AI related code in your minus states? Or maybe extra copies of the guard states (although I doubt this)?

[State -1, AI_ GUARD]
type = ChangeState
value = 130
triggerall = var(59) = 1
triggerall = InGuardDist
triggerall = statetype != A && statetype = S
triggerall = ctrl
trigger1 = !(enemynear,hitdefattr = SCA,AT)
trigger1 = random < ifelse ((p2stateno=[200,1999]),750,ifelse((p2stateno=[3000,3999]),999,900)) ;This random line is based on a Rajaa KOF char

Go to MUGEN.cfg and find this:

Spoiler, click to toggle visibilty

[Arcade]
 ;Set to 0 for computer to choose color 1 if possible.
 ;Set to 1 for computer to randomly choose a color.
AI.RandomColor = 0

Put AI.RandomColor to 0 and they should stay color 1 as long as they don't fight themself. In turns mode, if player 3 on your team is the same character, they enemy will be a different color too.

[Info]
name = "Name"
displayname = "Name"
versiondate = 08-2011
mugenversion = 1.0
author = "jjmugen"
pal.defaults = 1,2

[Files]
[...] ;all files stuff
pal1 = name1.act
pal2 = name2.act
pal3 = name3.act ;Secret Pallete

[Arcade]
intro.storyboard = intro.def
ending.storyboard = ending.def

[Palette Keymap]
x = 1 
y = 1
z = 1
a = 2
b = 2
c = 2
x2 = 3
y2 = 3
a2 = 3
b2 = 3

[State 0, LifeSet]
type = LifeSet
trigger1 = roundno = 4
value = 1