When adding a flag to the timeline several things are of note:
1. You can't use enter/return to close the dialog box once you've typed a flag id and description. In fact if you do and you click Apply to assign and close the box it doesn't close unless you click the close button.
2. My assumption would be that the dialog box would take over the workspace but that's not how it works. If you click away from it, say click on content manager or somewhere else within the workspace, the Add Flag dialog box hides behind the workspace and you can't access it again using the flag icon on the timeline. You have to move the workspace to find it hidden there. 
3. Why do I have to delete or create a whole new flag in the same position? Why can't I edit the name/description of one that exists? Oh, you can, but you don't know that unless you click "add flag" which opens your existing flag with existing name and description. UI issue.