Hi LightStar,
This is a easy one, this is because they are two different menus, the top settings are from the old skinning era,
like win 98 and XP, since Vista Microsoft introduced a second menubar style, the one at the bottom of your screenshot.
As I was explaining to another user early, you may know that SkinStudio let you use custom and experimental settings,
this is a great thing for skinning, the problem is that not everyone knows or tried everything so sometimes, mixed settings can
bring different results because sometimes on settings can overwrite another.
The thing is that right now the menu bars like "File, Edit, View, Help, Etc" are the section "Menu Bar Options", in fact "Menu Bar Options"
are in fact the "Menu Bar Buttons", and like the Toolbar sections, the buttons that command the text settings, not the Toolbar background,
the Normal state that defines the menubar text colour and the other states define the hover, pressed, etc, the things is that if the normal
state of the graphic is not present because the OS not use it or because it's possible to use it but the skinner make it invisible, the text there
is still the Button text and not the background text.
SkinStudio really need a cleanup but this may need some changes in WB too, and it wasn't really possible before because old skins
that still use old settings will not work right, now that XP and Vista are no longer supported, a clean up could happen, I think that the ideal
is to have a new SkinStudios separated form the actual one that would not have old settings at all, so if you need to edit a old skin, you go
with the old SKS, if you're making a new skin, you would go with the "news" SKS.
If you could tell me what exactly you want to do with the menubar and the selection colours, I can try to help you to achieve that.
Just to better understand what I meant up there, you can skin many parts in different ways, if you remove all the text settings from
the "Menu Bar Options" section for example, the menu bar (including the buttons) will start using the text settings from another part,
I'm not 100% sure right now without looking but I believe it will start using one of the Toolbar buttons text settings.
Anyway, let me know if I can help and I'll be glad to try 
