You need to get the hotfix for this issue.  Unfortunaly this is an unofficial hotfix.  This fix is in this thread from Bernard.

Hans,

  Thank you, works great.  This functionality is a big asset for this web application.

john

Your project works but mine doesn't but is more complex than your.  I have no idea what it causing the problem.  Not sure where to look, but this is killing my projects.

This is my grid settings.

<ISWebGrid:WebGrid ID="WebGrid1" runat="server" Height="320px" UseDefaultStyle="True"
                    Width="100%" DataCacheStorage="Session" EnableViewState="true" ViewStateStorage="PageCache"
                    EnableSection508Standards="False" RenderingMode="XHTML" EnableWebResources="Always">
                    <LayoutSettings AllowFilter="Yes" AllowGrouping="Yes" AllowSorting="Yes" PagingMode="VirtualLoad"
                        VirtualLoadMode="Default" GroupByBoxVisible="False" AllowColumnFreezing="No" AllowColumnMove="Yes"
                        AllowExport="Yes" AlwaysShowHelpButton="false" AllowSelectColumns="Yes" RowLostFocusAction="NeverUpdate"
                        AutoFilterSuggestion="True" FilterBarVisible="false" HideColumnsWhenGrouped="No"
                        InProgressUIBehavior="ChangeCursorToHourGlass" PagingSize="25" ShowFilterStatus="True"
                        RestoreRowSelection="RootTableOnly" VirtualPageSize="25" PagingExportMode="ExportAllData"
                        AllowMultipleSelection="No" GroupRowInfoFormatDefault="[caption] : [value] ([count])"
                        ColumnFooters="No" HeaderClickAction="SortSingle" ShowColumnAction="true" RowHeaders="No"
                        CellClickAction="CellSelect" AutoFitColumns="false" PersistRowChecker="false">
                        <FreezePaneSettings ShowInContextMenu="false" MaxFrozenColumns="1" AbsoluteScrolling="True" />
                        <ClientSideEvents OnAfterInitialize="OnAfterInitialize" OnUnhandledError="WebGrid1_OnUnhandledError"
                            OnResponse="doLoad" />
                        <AlternatingRowStyle Font-Names="Verdana" BackColor="#ECE9D8" Font-Size="8pt" HorizontalAlign="Center" />
                        <RowStyle Font-Names="Verdana" Font-Size="8pt" HorizontalAlign="Center" BackColor="#c9c9c9" />
                        <FooterStyle Font-Names="Verdana" BorderSettings-Left-Color="White" 
                            BorderSettings-Top-Color="White" >
                            <BorderSettings>
                                <Left Color="White" />
                                <Top Color="White" />
                                <left color="White" />
                                <top color="White" />
                            </BorderSettings>
                        </FooterStyle>
                        <StatusBarStyle BaseStyle="Normal" Font-Bold="True" Font-Size="9pt" BackColor="#b5d4eb">
                        </StatusBarStyle>
                        <TextSettings>
                            <TextItems>
                                <ISWebGrid:WebGridTextItem TextItem="CommonText/Refresh" TextValue="Refreshing Carriers" />
                                <ISWebGrid:WebGridTextItem TextItem="CommonText/NoData" TextValue="There are no Carriers to display, modify the filters above to view Carriers" />
                            </TextItems>
                        </TextSettings>
                    </LayoutSettings>
                        <RootTable Caption="Carrier Information" TableHeaderVisible="False" DataKeyField="DOT_NUMBER">
                        <HeaderStyle BackColor="#3d4351" BorderStyle="Solid" BorderWidth="1px" Wrap="true"
                            Cursor="Hand" Font-Names="Verdana" Font-Size="8pt" ForeColor="White" Font-Bold="true"
                            HorizontalAlign="Center" CssClass="WG5-Header" CustomRules="height:auto">
                            <BorderSettings>
                                <Left Color="#3d4351" />
                                <Top Color="#3d4351" />
                                <Bottom Color="#3d4351" />
                            </BorderSettings>
                        </HeaderStyle>

This is the button click code:  The first time is fine, if I select other records after postback, the count of CheckedRows includes the records from the first attempt.  This is also occurring when using a group by.  I am also filling the gris using the InitalizeDataSource event.  Any ideas?  Is jQuery inteferring?

    Protected Sub btnAssign_Click(ByVal sender As Object, ByVal e As System.EventArgs) Handles btnAssign.Click
        If Page.IsValid Then
            Dim checkedRows As ArrayList = WebGrid1.RootTable.GetCheckedRows()
            Dim textValue As String = String.Empty
            Dim dot_number As String = String.Empty
            Dim entry_date As String = String.Empty
            Dim ostate As String = String.Empty
            Dim day_90_date As String = String.Empty
            Dim audit_type As String = String.Empty
            Dim offsite_eligable As String = String.Empty
            Dim carrier_name As String = String.Empty
            Dim ne_status As String = String.Empty
            Dim ne_exit_date As String = String.Empty

            Dim success As Boolean = False
            Dim i As Integer = checkedRows.Count

            For Each keyValue As String In checkedRows
                dot_number = keyValue
                carrier_name = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("CarrierName").Value
                entry_date = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("EntryDate").Value
                ostate = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("OICState").Value
                day_90_date = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("Day90Ltr").Value.ToString
                audit_type = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("AuditType").Value.ToString
                offsite_eligable = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("OffsiteEligable").Value.ToString
                ne_status = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("NEStatus").Value.ToString
                ne_exit_date = WebGrid1.RootTable.Rows.GetRowByKeyValue(keyValue).Cells.GetNamedItem("ExitDate").Value.ToString

                success = AssignCarrier(i, dot_number, ostate, entry_date, day_90_date, audit_type, offsite_eligable, carrier_name, ne_status, ne_exit_date)
            Next
            ' clear the insput field
            clearFields()

            ' rebind grid
            'WebGrid1.RootTable.GetCheckedRows().Clear()
            WebGrid1.ClearCachedDataSource()
            WebGrid1.RebindDataSource()
            ' This forces a rebinding of the grid,  not a very good way but appears the CheckedRows are not cleared out!
            'Response.Redirect("~/SA/unassigned.aspx", True)
        End If
    End Sub

Nope it doesn't clear the checked rows.  It clears them from the Grid but if you look at the CheckedRows collection the previous selections are still there.