What do you mean embed in another .net app?
When you get the the 'Could not load class 'dijit.layout.BorderContainer' it's usually because of a javascript syntax error, like a missing ;, malformed code, etc. The reason you get the BorderContainer error is because it's the first thing dojo parses in your code. I suspect in your case there is some conflict when you put it all together. Post some code or the stack from the error.