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To ensure repeatable and consistent builds, I would recommend that your build process only use what is retrieved from source control for builds. I'm not sure where you're copying files from after checkout, but that sounds dangerous.
The recommended procedure would be to require developers to manually add new files to VSS when they check in changes to a project (when using the VSS IDE integration in VS6 or VS.NET, I believe it will prompt for doing this when adding an item to a project).
The SourceSafe.bld sample demonstrates automating bulk adding (for instance, to populate a new database from a local directory tree or to add a new project and all its files), but if you wanted to automate adding of new files to an existing VSS project, that is not so simple and there's nothing built-in to do it for you (other than possibly ignoring errors as you mentioned). You would need to write script code to parse and compare the local directory tree w/ VSS and then generate add steps for any missing files (skipping files that wouldn't normally be placed in source control).
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