Aftermath of replacing thermal paste and pads

I recently replaced my thermal paste with MX-4. I was not going to replace the pads BUT when I took the graphic card apart, it ripped into ~10 pieces sticking top and bottom. I took it apart really softly too. It felt like the pads were melted? It was way too squishy compared to the new Fujipoly 1mm I replaced it with.
Now here is the problem. As many of you guys know, GPU-Z has 3 different sensors to measure the temperature. For my primary ATI 5870, #1 would hover around 60s, #2 would hover around 70s, #3 would hover around 60s again.
For my second card, #1 would hover around 60s, #2 would hover around 100s, #3 would hover around 60s again. This is on gaming not on idle. On idle, all of the temperatures on both card is around 40 to 45. I did my search and was told that it was NOT making fully contact with the heat sink? However, I put the original and the new thermal pads right on top of each other and they are exactly the same size. I'm not sure what is going on here anymore. I compared it with the 1st card which is functioning correctly and I mimicked the exact steps on to the second card.
Anyone have any clues? I can't go back to the original pads, it's all torn up.

 

One more thing. My second graphic card is now idling at CPU Core Clock of 405 MHz and GPU Memory Clock of 1000 MHz. After ~5 minutes, it drops down to 300 MHz and 400 MHz respectively. I thought second card doesn't even get used until full screen mode on games?

 

This is correct, the driver will only actively use the 2nd gpu on a full screen based application.

Logic dictates that only a full screen application would need the calculational power to run the application at optimum speed but, sometimes when using a GPU intense application thats runs windowed (native resolution) will also kickstart the 2nd GPU.