It’s like everything you place behind scripts is just added to the default theme location. In this case it now has two slashes behind www.mysite/sites/all/themes/mytheme.
There doesn’t seem to be a way to have it move up the directory tree when I use scripts?
I now did it by placing a libraries folder inside my theme folder (where the other files/images etc. also are) and direct it simply to that directory. with scripts libraries/swfobject/swfobject.js.
But how is it done with other scripts then which use this libraries folder which is at www.mysite.com/sites/all/libraries? It now has the nivo-slider script in it for example. I thought it might be convenient to place all javascripts in there, but how do they make it direct upwards from mytheme > themes to libraries then?
Oh, I see what you mean… The script line isn’t parsed as a path, it’s a piece of text that is attached to the site root + path to theme and printed to the html template. I didn’t expect that.
It’s not as clean as adding it to the info file but you could add your file directly to html.tpl.php (D7) or add it using a block with the drupal_add_js(); function.