The bars defined in the Bar Styles dialog box over lay one another, with bars lower down in the list overlaying bars above it.

If the Flag2 definition is below the Flag1 definition and you have both Flag1 & Flag2 set to yes, the lower (Flag2) bar overlays the Flag1 bar. You can show multiple bars if you use the thinner bar shapes if you want a task to show for both Flag1 & Flag2. If you have kept the "Task" definition, make sure you change the Show For... section and add Not Flag1, Not Flag2, Not Flag3.