I think the FE is suggesting, quite rightly, that a frequent source of genuinely malicious script is in spyware, for the detection of which Spybot and AdAware are very good free tools. Malicious script warnings generally refer to activity which has a virus like pattern, but hasn't been identified as a recognised virus, and so it could well be a false alarm.
There may be an entry in the startup list (Start - Run - msconfig - Startup) that is calling for the suspect script to be run. If it is, then you need to disable it. Try initially disabling all unnecessary startup items.