'Newly Added File' and VSS
So, we have a handful of files in our project that we do not want to check into VSS. We see this pretty little red check next to them stating 'Newly Added File' and, every time we do a project check in, we have to make sure we unselect these files.
To disassociate these files with VSS, we did:
File > Source Control > Exclude (filename) From Source Control
And now we are good. Many thanks to Ivan Towlson at White Carbon for the tip!