A lot of these virus scanners detect threats based on several things; some of them are as anal as to detect by filesize and type...
so if you have a file that's say 23k with the extension ".js" and a similar name to something in its bank, it'll flag it as a virus.
They can detect by "signature" which will check mainly filesize, name, extensions, etc; I highly doubt your site has a "trojan" in a javascript file... You should however open the file in notepad and see if, by any chance, there is anything "not kosher" with the file; though again, i highly doubt there is anything wrong here other than an anal retentive virus scanner.
