per pixel buttons have to be moved to be seen..........in their alignment settings. If your not seeing your buttons once you have applied your skin, then it COULD be the perpixel buttons you are having problems with.
Also Ive noticed you only have 4 buttons showing......normally there are about 13 or so, and there is a way to only have 4 like you do. (I dont know how that is done....apparently there is a technique to that, )
maybe somewhere along the line that is why your buttons are not showing up.
For perpixel buttons, they also need to be in a set of 8 for each button. normal, pressed, mouseover and 5 disabled buttons.
The titlebar buttons only need to be a set of 3. normal, mouseover, pressed, and then another set for disabled.. disabled, disabled, mouseover.
i hope this has helped.