Not an answer yet, needed to show the images, well I tried the same, used this code in aspx: (I did not change any setting in IIS, nothing in aspx as well, created a plain solution >> added the treeview and deployed.)
<asp:Content ID="BodyContent" ContentPlaceHolderID="MainContent" runat="server">
<div>
<asp:TreeView ID="TreeTest"
EnableClientScript="true"
PopulateNodesFromClient="true"
ExpandDepth="0"
ShowLines="true"
ShowExpandCollapse="true"
ShowCheckBoxes="Root"
OnTreeNodePopulate="TreeTest_TreeNodePopulate"
Width="1px"
runat="server">
<Nodes>
<asp:TreeNode Text="Something">
<asp:TreeNode Text="11"></asp:TreeNode>
</asp:TreeNode>
<asp:TreeNode Text="Something">
<asp:TreeNode Text="11"></asp:TreeNode>
</asp:TreeNode>
<asp:TreeNode Text="Something"></asp:TreeNode>
</Nodes>
</asp:TreeView>
</div>
</asp:Content>
Checked in my local could see this:
Deployed in IIS version 6.2 , windows server 2012, could see this:
There must be something else which is preventing the checkboxes in your page. Show more code.