Checkbox issues in jQuery dialog and repeater

Thus, I basically beat my head off the wall for a while. Excuse me if I throw too much code, I don’t know a better way to explain this. I have a repeater with ItemTemplate from:

<ItemTemplate>
    <div id='FileFrame<%#Eval("Id")%>' class="view">
        <userControl:ConfigFiles ID=<%#Eval("Id")%> runat="server" />
    </div>
</ItemTemplate>

Some jQuery that set a dialog box for a div.

$(document).ready(function() {
        $(".view").dialog({
            autoOpen: false,
            title: "Configuration Files",
            buttons: {},
            height: 600,
            width: 800,
            open: function (type, data) { $(this).parent().appendTo("form"); }
        });
    });

and some more jQuery that open the dialog.

$("#FileFrame"+ConfigId).dialog('open');

Now the user control contains a bunch of flags inside other repeaters along with the "Load control cells" button. The problem is that when I look through the debugs and click the button, none of these flags are ever read as checked, unless I set Checked = "true" on the aspx page.

Here is a snippet of code where it cannot do what I thought it should do.

foreach (RepeaterItem item in FilesRepeater.Items)
    {
        CheckBox box = item.FindControl("DownloadFileCheckBox") as CheckBox;
        if (box.Checked) //<-- always false unless I set it to true in aspx,
                         //    then it always true
            {/*do work here*/}
    }

?