i also faced this issue today. The method for sorting checkboxes uses the column-index to indentify the column to sort. This index seems to be broken, because the fixed columns are not recognized.
You have to substract the number of fixed columns from the iColumn value.
/* Create an array with the values of all the checkboxes in a column */
$.fn.dataTableExt.afnSortData['dom-checkbox'] = function ( oSettings, iColumn )
{
var aData = [];
/* iColumn -= {number of fixed columns}; */
$( 'td:eq('+iColumn+') input', oSettings.oApi._fnGetTrNodes(oSettings) ).each( function () {
aData.push( this.checked==true ? "1" : "0" );
} );
return aData;
}
This could be a quick fix until the problem is solved.