Kwicks not working after permalink change

I’ve recently started working with WordPress and as these things go along I’ve encountered my first real problem.

I’ve made my own theme and it has a kwicks menu build in, kwicks works with jquery and it’s own javascript file.
the javascript files for it are in the same directory as the other javascript files that wordpress has.

And the javascript files are called in the header.php file, which in turn is called on every page.

And the menu worked fine..
The problem is, ever since I changed the permalinking to custom and show
/%postname%/ instead of the pageid’s that are generated, the menu stopped working on all pages except for the homepage. (which is just the base url).

Does anyone know what the connection is between these two?
Is the linking to the javascript files different when you change this?

It’s a bit odd since the css files and images for the layout all link correctly, but it seems like the javascript can’t be found for those pages.

Any help would really be appreciated.
Thanks in advance.

~ Gerben