Yes, I have your files, but using them causes errors, since you're creating a dynamic menu and I don't have the connection file, so I have not used them. Also I have not been able to reproduce this on any menus that I have created.
A test you can try is to open a new page and apply a new menu. Keep the menu simple and generate a menu with a main level and 2 sublevels. Try using static links to keep it simple. Change the width of level 1 and see if the problem is on this simple menu as well. Keep everything default on the menu other than adding links to make it have 2 sublevels and changing the width.
If the menu works, then we will know that it is caused by another setting in the wizard that you had previously changed, and not the width and padding calculations.