AWS and custom jQuery scripts

I’m using AWS plugin for the first, I found it works very well in most cases if you don’t want just a nice transition effect on pages, but a true ajax transition without loading all stuff in every single page. The problem is that I’ve got some custom jQuery fuctions effecting elements inside the ajax div. So they work just at the first load. I wonder: is there any way to exclude single files – as custom.js f.e. – and prevent them to be ‘static’ but reload them every time?
Other wise I should put all scripts inline (I wouldn’t like it) or uninstall AWS.
Thanks for your help.