There was a concern by some users why SkinStudio shares a start menu with the original substyle when you create another substy;le based on it..
Basically the answer is - It's not a bug - It's a feature. It's like that by design. If you select a prefix on save then you will get another start menu as well, otherwise skinstudio will use the same stuff for 2 reasons.
1) it does not know how to name the new "xpstuff.xp".
2) it does not know whether you really want to break the connection. You may as well want to just make a variation of your skin with slightly different titlebar buttons.
But imagine it did that so 2 things happen - you didn't specify the prefix to create new images so once you change the images in one substyle you change them in the other too since you didn't tell it to make copies of them. Now imagine how outrageous it would be. "But it uses another xpstuff.xp" you would say. "Why one substyle breaks the other substyle images" you would say. And you would be right. if everything's duplicated then everything is duplicated, if nothing then nothing.
Now let me show you the solution to the problem. I usedto direct people to the "Code" tab forgettig that the combo for "non image" file references is actually editable. But today I've read an easier sollution, by Tiggz:
When you want the substyle to have a different start menu, after you create the new substyle you need to click "taskbar" in the navigation tree in the left hand side of the window, then over on the right click on the word file, and then below, in the "value" text entry field you can change the name from the default (XPStuff.xp).
Keep your great skins coming!