I have noticed the same problem.  Downloads of compressed files from legitimate sources are identified as being infected with WS.Reputation.1 and subsequently deleted.  I typically use "download statusbar" add-on in FireFox 3.6 and have this configured to automatically scan all downloads with NAV17.6.0.32\navw32.exe. As soon as the download is completed, NAV scans the compressed file,  identifies it as infected and deletes the file.  The problem seemed to arise with a program update from 5/5/2010 or 5/6/2010.

My systems are running Windows 7 Ultimate 64-bit using NIS2010 for AV protection.  Other malware programs (Iobit 360, PC Tools Spyware Doctor/Threatfire, VirusTotal) do not identify any type of risk in the same files.