Glenn:
When i started with SCM I also had several problems, but now is everything fine. The thing is that when someone checks out a file, and you want to check it out also, it gives you some options that sometimes we dont read, but it is telling you that you will check out the file in test mode, that means that you cannot check in that file.
And as I did, you probably think you could get away with that but you cannot.
What i did, when you are at a certain point, that you dont know how to fix it. I disconnect the project from SCM, you can do that at
SCM -> Remote Work -> Disconnect for a mobile use...
Then you can create another DataBase in your server and do an "add the entire project to SCM"
Hope it helps.
Andres Sanchez