Found an interesting one today on this old topic.
As you know you can skin your custom controls by adding a <%@ Register tag in your skin file.
This works great.
But today I made a new company template and no way to make it work!
As soon as I add one of my custom control definition in the skin file I get an error :
"Type FooCompany.Agile.Web.UI.WebControls.XYZ is not defined".
After 30min of headache I managed to make it work.
The problem was the Namespace containing my controls is FooCompany.Agile.Web.UI.WebControls and the Theme containing the skin is named FooCompany.
So I renamed my theme FooCompany_Design and everything is fine.
Just after that I googled and (of course!) found that the problem was already solved 1 year before there :
Information is power, that's why Google rules the world.