1. Make the flat sheet the way you want. Then add bend lines and bends where you want. Don't use the flange command.
2. If you use flange commands. Set them up to have the bend outside the main tab. To make this easier, I typically make the tab a bend radius and thickness small on the sides with flanges. Then when the flange is compleatly ouside the tab, your back the the origional desired size.
3. If the 2 way cornerner does not work, do a manual cut inside the corner point of the bends.
Note: I do sheet metal in orderd only, not sure about Sync work arounds.
I attached 3 files so you can see the varius methods. In the 3rd file, check out removing the cut.
edit. I didn't take into account the varius angles of the flanges, so the 2 way corner command may not work. If both flanges are the same style of contruction, the 2 way command should work at any sets of angles.