It might be thread-necromancy, but as I was also stuck with this, here's my solution for the developers out there struggling with this issue:

The contents of a container control can usually be found in the container.Controls property. That has an AddRange() method that takes a collection of Controls as parameter. The FlowLayoutManager does not do any sorting, but keeps the order in which the items were added. So I ended up with ordering the items the following way: I made a List<Control> instance, added the required controls in the required order (I had to do a bottom-up order with some inserting here and there, a list seemed the perfect choice) then exported them as an array for AddRange() with the List.CopyTo() method. So the final code looks something like this:

private var controlList = new List<Control>();
private var anUltraPanel = new UltraPanel();
private var aFlowLayoutManager = new UltraFlowLayoutManager();

[...]

private void createReverseUltraFlowLayout() {

this.controlList.Insert(0, item1);
this.controlList.Insert(0, item2);
this.controlList.Insert(1, item3);

this.anUltraPanel.ClientArea.Controls.Clear();
Control[] controlArray = new Control[this.controlList.Count];
this.controlList.CopyTo(controlArray, 0);
this.anUltraPanel.ClientArea.Controls.AddRange(controlArray);

}

and the output should be something like this:

Item2
Item3
Item1

The Clear() and AddRange() solution might not be optimal, but that's the best I could come up with.

Is there anyway to accomplish this at run-time?  I need to order the controls based on the user defined order that is stored in the database.