There are three main reason why you are missing your message flags
  • You are using Hotmail or another account type that doesn’t support flagging messages.
  • The Quick Flag column has been hidden. To show it, on the Viewmenu, point to Arrange By, and then click Custom. Click Other Settings, and then under Other Options, select the Show Quick Flag column check box.
  • Your Flag Status Field is not shown. To show it, on the View menu, point to Arrange By, and then click Custom. Click  Fields, and then under available fields select Flag Status and press Add Button then press Ok.