Read the source and found a quick fix.
Add the code of line
ts.p.selarrrow = [];
to clear the selarrrow on header checkbox click.
It should be line 1994 of grid.base.js
$('#cb_'+$.jgrid.jqID(ts.p.id),this).bind('click',function(){
ts.p.selarrrow = [];
if (this.checked) {
$(“[id^=jqg_”+ts.p.id+”_”+”]”).attr(“checked”,”checked”);
…
