The newest version of FlyTreeView contains
FlyTreeView.PostBackOnCheck and FlyTreeView.PostBackOnUncheck
It was published today, and is already available at downloads:
http://www.9rays.net/download.aspx?productFamily=TreeView_ASP.NET_2
You have two options to handle check/uncheck:
1. Use FlyTreeView.GetCheckedNodes() to get checked nodes.
2. Handle FlyTreeView.NodeCheckedChange event. This is a special node-level event that is fired when treeview loads post data (before page_load).