I have used Speccy and I love it, I just recently built an X79 , Asus Sabertooth system with a 3960X chip and Speecy is reporting way wrong system temps.
I'm experiencing something similar. I recently upgraded to an X79 motherboard and CPU and now Speccy has no clue what's in my system. With my GPUs (two ATI 6870s), Catalyst and GPU-Z see both cards and show that they're in CrossFire. GPU-Z is able to pull the temps even. Speccy can't see the temps and doesn't see that the cards are in CrossFire. Also, I no longer am able to see my hard drive temps which blows.