the speed difference go like this from slowest to fastest.
graphical client, console, service
for the service it doesn't matter if you used the grahpical or the console or screensaver to install it, because they all run the same way.
a little secret i use to fold even faster then a service install is to change the username to Xevuhtess7. i got roughly 23 seconds faster on each frame by doing that, you should give it a shot