I have an ASP.Net CheckBoxList control inside an Ajax UpdatePanel.
I will include the code (C#) along with the HTML below.
I have found that it is something with the CheckBoxList not persisting through the post back.
BTW, it is a little messy. It is a prototype.
This is the method used to populate the original CheckBoxList
protected void BindCheckboxes()
{
    chkBuildings.Items.Clear();
    chkNeighborhoods.Items.Clear();
    string city = ddlFindHome_Location.SelectedItem.Value.ToLower();
    ResidentDataContext rdc = new ResidentDataContext(Utility.Lookup.GetResidentConnectionString());
    var neighs = (from n in rdc.spNeighborhoods where n.vchCity.Equals(city) select n);
    foreach (var neighborhood in neighs)
    {
        ListItem li = new ListItem();
        li.Value = neighborhood.intNeighborhoodID.ToString();
        li.Attributes["onclick"] = string.Format("document.getElementById('{0}').click();", btnNeighHack.ClientID);
        li.Text = neighborhood.vchNeighborhood;
        chkNeighborhoods.Items.Add(li);
    }
    var builds = (from b in rdc.spBuildings
                  join nb in rdc.spNeighborhoodBuildings on b.intBuildingID equals nb.intBuildingID
                  join n in rdc.spNeighborhoods on nb.intNeightborhoodID equals n.intNeighborhoodID
                  where n.vchCity.ToLower().Equals(city)
                  select b).Distinct();
    foreach (var buildings in builds)
    {
        ListItem li = new ListItem();
        li.Value = buildings.intBuildingID.ToString();
        li.Text = buildings.vchName;
        chkBuildings.Items.Add(li);
    }
    upNeighs.Update();
    upBuilds.Update();
}
BindCheckboxes() is called from:
protected void ddlFindHome_Location_SelectedIndexChanged(object sender, EventArgs e)
{
    BindCheckboxes();
}
This is the post back method for populating the Check Boxes of another CheckBoxList
protected void btnNeighHack_Click(object sender, EventArgs e)
{
    List<int> neighs = new List<int>();
    foreach (ListItem li in chkNeighborhoods.Items)
    {
        if (li.Selected)
            neighs.Add(Convert.ToInt32(li.Value));
    }
    ResidentDataContext rdc = new ResidentDataContext(Utility.Lookup.GetResidentConnectionString());
    var builds = (from b in rdc.spBuildings
                  join nb in rdc.spNeighborhoodBuildings on b.intBuildingID equals nb.intBuildingID
                  where neighs.Contains(nb.intNeightborhoodID)
                  select b.intBuildingID).Distinct();
    foreach (ListItem li in chkBuildings.Items)
    {
        li.Selected = false;
    }
    foreach (ListItem li in chkBuildings.Items)
    {
        if (builds.Contains(Convert.ToInt32(li.Value)))
            li.Selected = true;
    }
    upBuilds.Update();
}
Here is the ASP.Net HTML
<asp:UpdatePanel ID="upNeighs" runat="server" UpdateMode="Conditional">
    <ContentTemplate>
        <div style="font-weight: bold;">
            Neighborhood
        </div>
        <div style="padding-top: 7px; padding-left: 3px;">
            <input type="checkbox" id="chkNeighborhood_CheckAll" />Select All
        </div>
        <hr />
        <div>
            <asp:CheckBoxList ID="chkNeighborhoods" runat="server" />
            <asp:Button style="display: none;" ID="btnNeighHack" runat="server" 
                onclick="btnNeighHack_Click" />
        </div>
    </ContentTemplate>
</asp:UpdatePanel>
<asp:UpdatePanel ID="upBuilds" runat="server" UpdateMode="Conditional">
    <ContentTemplate>
        <div style="padding-left: 6px; padding-top: 5px; font-weight: bold;">
            Building
        </div>
        <div>
            <asp:CheckBoxList ID="chkBuildings" runat="server" />
        </div>
    </ContentTemplate>
</asp:UpdatePanel>