I moved this post from the developer forum to the design forum.
For anyone to help you will need to give more detail about the problem or post a link to the site where someone could see it.
If you changed from .NET 3.5 to .NET 4 as part of your upgrade then the article The Trouble With ASP.NET Menu may help you.
If you are just using the included skins you may want to copy the latest versions from /Data/skins into /Data/Sites/1/skins
You should also review the sticky thread about important skin changes.
Hope tha helps,