Virus scans are not 100% and often times you will need multiple scans and may be even different softwares to get rid of everything because not every antivirus is designed to get rid of every type of malware, there are just too many.
ALso if you did the scans in windows, many viruses are able to mask their presence after windows load up, so while you may get some of the items, you didn't get them all cause the anti-virus program cannot see them all. If you boot into safe mode and run the scans, most viruses can't load up and thus are more easily detectible and removed.
I would suggest you have your anti-virus program and download the free version of "Spybot: search and destroy" this second program takes a lot of adware and malware...