First of all, you haven't said anything that indicated that a virus is the cause of this, so I'm not sure that's related.
Ok, as to the part where you see can't see folders you think are there you might want to try enabling the view of hidden and system files (from Windows Explorer > Tools > Folder Options > View). You can also use utilities to investigate the file use like: http://windirstat.info/
Now as to the part where it says you need permission to delete, that's most likely because some process is using a file you are trying to delete, or you are trying to delete a file that you don't have permissions for (e.g. if you aren't logged in as an administrator). You can try booting into safemode to delete files but make sure you aren't trying to delete things that Vista legitimately is trying to protect you from deleting.