invisibility on external hard drive

Up until today I was a big supporter of Security Essentials but after last scan of my external hard drive am not so sure, it appears books in mobi and mp3 from j to z bog the software down bearing in  mind these files are small and now for my trouble I have still got 1.5 tb left of 4tb its just that I cant see it all and if I save an mp3 that begins with a k it saves invisibly  so have you any ideas I have a lot of music which holds special place for me and its doubtful I could find it again and besides that there has never ever been a problem with security essentials before even to the point I've found it reliable and helpful in past. Its annoying though the drive says its as full as when scan started but a lot of its now invisible .I have not played or done anything different now or in the last two years.I learned early on in my computer use that you don't mess or tweak with what's working to do just that keep it working.