The version you are working on is no longer the same as the version in the Vault database. The status icon changes from a check to a check mark with a green background. This tells you that the file is newer than the one in the Vault.
The Settings button in the Check In dialog box specifies whether or not to include children when checking in the file. By default, Include Children is enabled, which is recommended.
The icons for all files change back to the empty circle.