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When you try to add multiple projects to your department using the "Manage Team Member" option of mass edit feature in Web TimeSheet, you may not find the name of your department in the "Manage Team Member" drop-down.  Check print-screen "Departments not shown on Project Team Member  list.PNG" attached to this solution.
-When "Hierarchy filtering" is enabled users can only view, add, and edit projects in their department and their department's sub-departments.  
-Hence the projects which you are trying to add belongs to a different department so the name of your department is not seen in the "Manage Team Member" drop-down.
Edit the project and add your department to the "Visible to Departments" list.  Check the print-screen "Departments added to visible to department list.PNG" attached to this solution.
This is not an issue but this is how the application behaves when "Hierarchy Filtering" is enabled.