Since no one answered, and I've found a solution, here it goes, this fixes the problem:
viewToAdd.setBackgroundColor(Color.TRANSPARENT);
// make the required params object for the HUD viewToAdd
WindowManager.LayoutParams params = new WindowManager.LayoutParams(
WindowManager.LayoutParams.WRAP_CONTENT,
WindowManager.LayoutParams.WRAP_CONTENT,
WindowManager.LayoutParams.TYPE_SYSTEM_OVERLAY,
WindowManager.LayoutParams.FLAG_LAYOUT_IN_SCREEN | WindowManager.LayoutParams.FLAG_NOT_TOUCHABLE | WindowManager.LayoutParams.FLAG_NOT_FOCUSABLE | WindowManager.LayoutParams.FLAG_NOT_TOUCH_MODAL,
PixelFormat.TRANSPARENT);
params.gravity = Gravity.RIGHT | Gravity.TOP;
WindowManager wm = (WindowManager) getSystemService(WINDOW_SERVICE);