I just checked on the very simple sample with DataSourceID bound GridView and enabeld viewstate.  unfortunatelly, GridView loses both checkboxes value and viewstate of any controls in templated columns if you switch gridview to edit mode.

I cannot find aney easy workaround, so I think the best is to find a way to set the correct checked state on second databinding. (perhaps as I suggested earlier to save and restore their state)