Just because scans tell you that you are clean doesn't mean you are. They rely upon signatures.... That means that the malicious code you _might_ have on your system has to be recognizable by the scanning system. If there is no signature then there is no detection. If there has been some kind of rootkit installed you probably won't be able to detect it for yourself either.

Take a look around here and see what you can do for yourself. If there seems to be nothing you can and you are convinced that there is an issue then think about a reformat and re-install...

PS: don't forget to backup your _data_ files first...