Sorry for the double post, but I just made a discovery that, as far as I can tell, means the whole team has been doing it wrong from the start.
-local
Use configuration files from local directory. This option has no meaning on Linux, but is vital on Windows and Macintosh for running multiple clients on a machine. It instructs the client to read its config information from the client.cfg file in the current directory rather than, on Windows, from the installation directory specified in the registry, or, on Macintosh, the Library/Folding@home directory. Information such as the user name, team name, proxy information, machine ID are maintained in the client.cfg file. The flag ensures that work does not conflict. Use "-local" only if you are planning on running more than one instance of Folding@Home on the same machine (this is only useful if you are running on a multi-processor machine). Create as many directories as there are processors on the machine, copy the exe files and client.cfg file into each of these directories, run "FAH3Console -local -config" on each and specify unique machine IDs for each directory (under the Advanced Settings option). From then onwards you may run each copy by switching to its directory and running with the -local flag.
Now, if you're going to fold ATI and NVIDIA together, you'll
definitely need this, as some of the threads I've been reading say that 2 of those cards on the same system will fold both ATI and NVIDIA work units. According to Stanford, (this is more or less, couldn't refind the quote) 'its promising to see both architectures can fold each others WUs, however the results it returns are completely useless to us at this time'.
Anyways, its apparently required for multi GPU systems, so my rigs will be getting this flag put in pronto. I haven't seen any errors without the flag, but who knows? Maybe it'll give me an extra 100000 PPD a day.