That’s weird. Haven’t tried winrap, but sourceforge is known to be a reputable site.
Might just be a bug of the program. Might want to ask in the program’s forum to see if it’s a known problem: http://sourceforge.net/projects/winrap/forums/forum/1010364
As for the viruses in the chest, you don’t have to do a darn thing. When they’re in the chest, they are completely disarmed and harmless to your computer. Leave them in there if you want, for as long as you want. If you know that they aren’t false-positives and don’t care for them being on your computer any longer, you can just delete the files from the chest.
As a general rule though, we usually recommend to keep files that have been identified by avast as a virus in the chest for 2 weeks. That allows you to decide if the files were important or not, allows you to scan them later with newer virus definitions (to make sure it wasn’t just a false positive), or what-have-you.
If you delete them, there’s no way of getting them back, so hold on to them as long as you need to.