Well, I recently installed a new SLK-900 heatsink, and this exact same thing happened to me. Like I always do when installing a new heatsink, I hand-adjusted and eyeballed the fit to make sure the HSF had good contact. It did.With the case off its about 5-10C cooler. However, my mobo was halting with the case off because the CPU got to 100C with the Nexus AXP3200.
The temperature I reported was 75C. Even now as I sit its 80C with my stock fan, and I'm just sitting in BIOS (i.e. not running anything). I read on other forums that Chaintech measures on-die temp, while most other mobos report externel. This was supposed to account for the extra 10-15 degrees.
However. After booting up, the machine shut itself down in about 30 seconds. Weird, I thought. Then I went into the BIOS and checked the CPU temps: 70c at idle! That's strange, I thought: I know I mounted the heatsink correctly on all 3 lugs on each side, and I oriented it the correct way-- with the wide edge aligned with the wide edge of the socket.
I am not a newbie by any means, I've been building computers for years and years. The source of this particular problem, I think, was trying to "recycle" the existing ceramique thermal paste on the die. In other words: not enough thermal paste. Even though I scooped up as much as I could with a thin plastic card from the old heatsink, and transferred it to the surface of the CPU where it LOOKED like a sufficient thin layer, it wasn't.
When I removed the heatsink to diagnose the problem, the small amount of thermal paste had spread into a spotty, thin film on the heatsink bottom and CPU surface. I applied a generous amount of new paste and re-mounted the heatsink the same way I did before and-- poof! problem solved. Back to ~40c idle in the BIOS.
This is why the commonly offered advice to use the thinnest layer of thermal paste possible is MISGUIDED and possibly even dangerous.
What's particularly silly about that advice is, even if you use way too much thermal paste, the pressure of a correct HSF mounting will squeeze all the excess out anyway. At worst, all you've done is make a mess... whereas if you use too little thermal paste, your CPU will quickly overheat to 100c BIOS shutdown levels, as mine did! Or, heaven forbid, your BIOS can't detect the die temps and you overheat or damage your CPU. The risk of using too little paste is far more real and dangerous than the myth of too much thermal paste.