The reason we did this was so that a user could use any wsdl file without dealing with wsdl includes (which at the time of our initial design were not standard yet).
The best way to work around this is to specify a namespace with the wsdl.exe command. Accessing by web reference automatically does this but the command line doesn't. So for LocalLB.VirtualServer.wsdl do something like the following
wsdl.exe /namespace:LocalLBVirtualServer LocalLB.VirtualServer.wsdl
Do the same for the rest of the WSDL files you are working with and then each of the interfaces will be uniquely defined.
-Joe
Nimbostratus