Waiting and get_header('2')

I’m trying to get some JavaScript aspects stored in my header-2.php to work. It’s strange because the js doesn’t appear to kick in unless I leave the page open for maybe 5 minutes and then refresh it.

To be honest, I don’t know if this is because I’m trying to use a second header, there are a number of things that could be to blame, but any help would be appreciated!