I found out why my SLI GTX 480s were taking on average 1100 seconds to complete the beta work units. I turned off SLI and that did the trick. My last few work units have completed in 700 seconds at stock speeds. Oddly, it still shows my gpu clock speed as .81ghz. I've noticed other users will get this to 1.4ghz or so.

My gpu usage is around 55% for both cards.