I do Folding@Home (with a different group, sorry), and I recently discovered that I had a unit that wouldn't send for two weeks straight. Researching, I discovered that the version I was using (5.03 or something) was pretty outdated. Apparently 6.20 came out in like August 2008, and the newest version 6.23 came out in December. I don't really know if having the old version was responsible for my problems or not, but I figure if they have an updated version, they probably would prefer that I use it. If you're not sure what version of F@H you're using, you can right click the system tray icon and choose Status -> Log File, or search your computer for a file called FAHlog.txt. When you open that file, it will tell the version you're using somewhere near the top.
The message Sony & Folding put out when Folding was taken away read to me like "PS3 users have given us all the packets we need, we'll just be be working on analyzing the date, thanks!" and so there was no need to really continue on.