Password protected files are not for worry. The majority of the files are protected by some program (for example, Spybot) to keep your system save and for the antivirus do not show them as positives. No worry: virus can only be active when extracting it from an infected file. That were not infected ones 8)
I think not. Can you delete all your temporary internet files? (generally Tools > Options > some option for deletion…)? Do you have any program that automatically delete that files (for instance, BeClean, Internet Sweeper…)?