It is a bit old, this post. But this is my code to show/hide the columns. I use the built in function to display the columns and just mark them.
Function that displays columns shown/hidden columns. The #jqGrid is the name of my grid, and the columnChooser is the jqGrid column chooser.
function showHideColumns() {
$('#jqGrid').jqGrid('columnChooser', {
width: 250,
dialog_opts: {
modal: true,
minWidth: 250,
height: 300,
show: 'blind',
hide: 'explode',
dividerLocation: 0.5
} });