If you're using Visual Studio to check in files to VSS, the IDE will lock-up when checking in files as it has to check the status of all the files in the solution. Instead, if you know specifically which files were checked out, you can check them in individually.
Another approach is to Right-click the solution and select View Pending Checkins - this opens up a dialog that works asynchronously i.e. it doesn't prevent you from working normally while it finds the list of files to be checked in. To check in the files, click the Check In button on the Pending Checkins dialog.