I wrote an article recently regarding the hot fix released by Microsoft regarding locking down MS XML Core Services (version 3,4,6) to set the resolveExternals property to false by default. Previously this was true. If you haven't read this article, you can here.
Of course this is a simple fix if you are still developing native apps using the MS XML Core Service libraries. Simply set resolveExternals to true before doing a XSLT translation.
This fix unfortunately a little more difficult if you have written you're own maps in any version of BizTalk using XSLT as you have no control over the MS XML Core Services library.
I'd love to post the source code for the tool here, but it belongs to our client so sadly I can't. It is a relatively simple process using the .NET DOM. As we are using MS XML 3 (in BizTalk 2002) to do the translation, we used MS XML 3 COM object to do a validation after the conversion had taken place. Bear this is mind!