I'm curious what processor he was running at the time. SETI@home comes in different performance levels. If you've got it running as an NT Service, it'll run faster than the Screen Saver version for 95/98. Also, the latest version "does more science" than the older version, and takes a longer time per work unit. It also has to contend with other apps that might be running at the same time.
I'm not saying that the comparison you ran wasn't valid, but benchmarks are not as straightforward as they seem sometimes.