You're using an ID to select the input when instead you should be using something unique.
You either need to change the ID to be unique (they should be unique in the DOM anyway), or change the name of the checkbox to something like...
<input type="text" name="nama_item[1]" value="" style="width: 200px;">
And change your JS in the pop-up to use this name instead of the ID...
window.opener.$("input[name='nama_item[1]']").val($.trim(nama_item));