Thank you for your answers,
What I really want to know is why the regular scan on windows did not work properly and only when I did the scan on boot it recognized all the files infected so I could delete them.
The curious thing is that, once I had the name of the file (trough scanning the boot), when I checked just the infected file on windows, Avast recognized the virus.
So far, I scanned my system with Avast several times (on boot an on windows) and with a pretty good anti-malware software and nothing else showed up.
Ah, of course I have all my backups up to date. DVD, Pen drive and HD.
Best regards