This happens from time to time. May be related to having multiple folders in a workspace but cannot confirm that.

Sometimes when you rename a project it renames it but then starts showing the old name. If you attempt to rename again the dialog that opens will show the new name, attempt to rename says the project with that name exists. If you remove the folder from the workspace and then add it again you will see the correct names but then after project discover has happened it shows the old name.