Well this is driving me crazy even if the code is right saving the skin in SKS 6 messes things up again. Anyway... heres a mini tutorial for anyone having the same problem as me

Hopefully it will get fixed in the next release of SKS 6.
Solution dont touch any of the shutdown/logoff parts in SKS6 do this last (if you are using SKS 6 as main editor) in SKS 5 and finalize your skin.
You need all in all 4 images 2 for the regular backgrounds and 2 for the per pixel ones. And it didn't work for me using the same image for both shutdown and log off bitmap and per pixel respectively. Also use short names for them less than 50 chars to be on the safe side.
Step by step.
1. Create your Logoff/Shutdown Size 313x198px
2. Save it as logoffbitmap.BMP and shutdownbitmap.BMP (if you are using the same for shut/logoff)
3. Save Perpixel backgrounds as logoffPP.PNG and shutdownPP.PNG
4. In SKS 5 Import/browse BMP's for the regular background and the PNG's for the perpixel ones.
5.Go to CODE, the tab in the top of the middle window. Click "Logoff Dialog" in tree view (In the "XP Shell" branch) And it will jump to where you need to be in the code. If you aren't there already.
6.Add "PerPixel=1" under "[LogoffDialog.Background]" and do the same for shutdown. Delete this under perpixel if there is such a line. This will generate a error if you analyze the skin but just ignore it.
And here is how the working code should look like.
(HideText=1 is optional ofcourse, it hides the "Log off windows" and "Turn of computer" text)
------------------------------------------------------------------
[PleaseWait.BackgroundPerPixel]
Image=Whitebear\WhitebearPleaseWait.BackgroundPerPixelImage.tga
PerPixel=1
TextShift=500
TextShiftY=0
[Screen.BackgroundPerPixel]
Image=Whitebear\WhitebearScreen.BackgroundPerPixelImage.tga
Trans=1
PerPixel=1
LeftWidth=610
RightWidth=600
TopHeight=500
BottomHeight=500
SmartSmallMargins=1
[LogoffDialog.Background]
Image=Whitebear\WhitebearLogoffDialogBackground.bmp
PerPixel=1
[ShutdownDialog.Background]
Image=Whitebear\WhitebearShutdownDialogBackground.bmp
PerPixel=1
[LogOffDialog.BackgroundPerPixel]
Image=Whitebear\WhitebearLogOffDialog.BackgroundPerPixelImage.tga
HideText=1
[ShutdownDialog.BackgroundPerPixel]
Image=Whitebear\ShutdownDialog.BackgroundPerPixelImage.tga
HideText=1
------------------------------------------------------------------