CSS & Javascript not working on all pages

[eluser]eperez[/eluser]
My site was recently compromised. I'm not a web developer, but through some guidance here and at another site I've pretty much fixed everything so far, except for one small issue.

This is my site: http://avertsoftware.com/

If you click on the "Download" link for instance, it will take you to the download page. ie: http://avertsoftware.com/download

CSS and Javascript load just fine. But if you click on any of the links under "Info", which is in a subdirectory called "info", they don't load the Javascript and CSS. The HTML on each page is identical to the working pages. I even copied a working page, renamed it to one of the others and tried it. It turned out just the same.

This leads me to believe that something was changed in the code igniter files.

Does anyone have any ideas about where I should look to see what has been changed? Or maybe something similar?

Thanks