From the looks of your code, clicking on the #customAttachments field is firing a jQuery event that calls a tb_show() method to load the media-upload.php file with certain GET parameters already set (post_id, type, TB_iframe). What you could do is add another GET parameter and check if that’s set in order to execute your add_filter() code.
So:
tb_show('', 'media-upload.php?post_id='+post_id+'&type=image&TB_iframe=true');
Becomes:
tb_show('', 'media-upload.php?post_id='+post_id+'&type=image&TB_iframe=true&myMarker=true');
Then you can use:
if(isset($_GET['myMarker'])){
add_filter("attachment_fields_to_save", "rt_image_attachment_fields_to_save", null , 2);
}
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