I'm not sure I understand well your question. You are trying to change from "3D" to "2D" in runtime or you change the property from the IDE?
For me it works fine when I choose the appropriate settings in the designer, as you can see in following screenchot:
As for the columns shown in the datawindow, yes they do not show lowered even if lower border is selected.
The first is not a 3-D Look. The second is. The screenshot was taken in a win 7 x64 and default theme with aero. The application is built with PB 12.5.2.
Andreas.