It seems that in modules > channels > mod.channel_standalone.php on line 427 where the script calls the frontend_filebrowser method of the filemanager class, it passes it a second parameter of true which determines whether the SAEF calls jquery.
However this is hard coded in the channel module and should be a parameter of {exp:channels:entry_form} because I need to load jquery in the head before certain other scripts are loaded, calling it this second time causes a conflict and my scripts stop work.