When you create a BizTalk project as a part of the Enterprise Template of Visual Studio .NET 2003, an additional .(dot) would follow the project name which you input.
For example, if you enter the “Project1” as the BizTalk project name, the generated project name will be “Project1.”, and the compiled assembly name will be “Project1..dll”, rather than “Project1.dll”. And, such name would cause some problems with other BizTalk tools such as BizTalk Web Services Publishing Wizard. Umm….I think the BizTalk project surely doesn’t support this scenario.
Anyway, when you create an Enterprise Template, be cautious of the BizTalk project's name. :-)

Thanks