I'm not really sure what the script at the very bottom of /assets/js/slides.js is doing, but I'd try taking the last 5 lines out and see if the cross fade thing still works. I seriously doubt that the "Browser Slide-Show script" has the need to obfuscate the JavaScript at the bottom. Someone wrote to this file.
If you have software that's able to write to slides.js, you have bigger problems. Get the security on the web server tightened up (apply latest updates, patches, check permissions, change passwords, etc).