I don't use flashget, but I would have thought the settings would allow for scan all of the files or allow use of wild cards, etc. If it doesn't, I would suggest trying another that does. If that suits your needs then you could switch permanently.
I use Star Downloader, I find that a very good downloader (works with firefox, avant and IE, context menus), if you select scan with your AV, the default is to scan all files.
Sorry I can't be of more help, not being a flashget user.