After a while I noticed that the PPD for each was very low (6,000) compared to the current database entries for GTX 460s found here: http://compdewddevelopment.com/projects ... ce+GTX+460. Upon investigation of this low PPD, I found that the GPUs were downclocking themselves from a core clock of 780 MHz (what they should be) to 450 MHz and then to 51 MHz. (I did not notice what other clocks it affected.) Heat was not the issue as running idle, one GPU is up to about 43C (that card is missing one of its two fans). Overclocking was not the issue as the cards are at stock clocks. I researched the issue and read in many places that it was an NVIDIA driver issue (or rather, a "feature") that was introduced somewhere just before the 3xx version drivers.
I searched for a solution to this unwanted throttling for hours. I came across a few suggestions, one of which was changing the "Power Management Mode" in the NVIDIA Control Panel to "Prefer maximum performance". I tried this, but to no avail. Another suggestion was to download RivaTuner and manually change settings (I think registry entries?) to forced-set values, but whatever I tried with that program didn't help. Tried different drivers, but went through hell in the process. By this time, I was getting quite discouraged and thought these cards would never fold correctly.
Then, I came across a forum post in one of my Google search results titled, "[GUIDE] Nvidia Inspector GTX670/680 - disable boost / fixed clock speed / undervolting". A program called "NVIDIA Inspector" has saved my sanity. I tried out the instructions in the forum post (which were extremely simple) and it the downclocking problem. Basically, you download the program, unzip the files, create a shortcut, and change the execution path to "...exe -forcepstate:n1,n2" (n1 is the graphics card index, n2 is the PState (0 is full)). Repeat the parameter for each GPU for which you want to force clock speeds. Execute the shortcut, and now you are free from unwanted downclocking affecting your folding performance! With the flags, no windows are opened, so what I did was copy the shortcut to my Windows startup folder and the clocks are automatically fixed every time I boot (I have yet to reboot to verify this, though it should work).
I have seen other threads about the/a downclocking problem, and I hope that if the methods proposed in those threads do not work for some that this method will. If you find yourself in the position I was in and you wish to try this method, read the guide linked to above first as it explains some other features like force-setting the clocks if you wish to also overclock.
Happy folding!
And now I just need to find out why my cards are still performing so badly...