Jose,
I've use MMortals and VSS - you're right it's not a pretty thing to work with. What we did is only check in the Application specific files while not "Including in Source Control" the framework files. The trick is to hack the PJX file by removing all the framework file saving them to a dbf, adding the project to source control then appending the records that represent the framework files.
Updates and compilations are alot easier in this fashion