Pondus
2
1. The quake2.exe file has been on my machine for years and was not infected before, so has a virus somehow altered the file on me (which could be a severe problem if it starts doing it to other files), or is this a false positive?
It is not detected as virus .... but suspicious
have you tested the file at www.virustotal.com
You can upload files and report issues to avast lab here: http://www.avast.com/contact-form.php (change subject according to Your case)
you can use mail
send to virus@avast.com in a password protected zip file
mail subject: False Positive / undetected sample (select subject according to your case)
zip password: infected
or you can send files from avast chest
how to use the chest. http://www.avast.com/faq.php?article=AVKB21