In Windows Forms, Transparent isn't. All that does is tell the control to take on the fore/back ground properties of the container that contains it.
For example, you put a Panel on a Form. If you set the BackColor of the Panel to Transparent, the Panel will take on the BackColor property of the Form. It does NOT make the Panel see-through.
There are some articles and forum answers out there that take you through making your own pseudo-transparent Panel control by not drawing the background of the Panel. This technique may or may not do the trick for you, depending on what's going on on your Form behind your Panel control.
c# - Any trick to use opacity on a panel in Visual Studio Window Form? - Stack Overflow
Make panel transparent