This is just a quick tidbit. I will expand in an article that I'm writing on BizTalk mapping and custom XSLT.
When you are using Inline XLST in a BizTalk map, if the document that you are working uses namespaces, you have to explicitly declare the namespace that the element(s) that you are building belongs to.
Compiling the map will not fail but you can run into some really nasty runtime issues that are extremely hard to debug.