How do you mean flickering? Do you maybe have a simple code example?
Possible you could set the form visibility to false temporarily when losing focus. (or set it transparent completely)
How did you implement this? If you didn't do it in the right way/order it is very well possible that the repaint from losing the focus skips your code and therefore is showing the form without transparency effect.
Try this in the constructor:
InitializeComponent();
this.SetStyle(
ControlStyles.UserPaint |
ControlStyles.AllPaintingInWmPaint |
ControlStyles.DoubleBuffer, true);
Also, have a look at this:
Transparency Tutorial with C# - Part 3[
^]
Good luck!