This is my same problem.
i have GTX 560 Ti too and i need to boost with afterburner otherwise skyrim crashes in a few minutes at ultra-high settings.
there is a way to run enb with afterburner or an Oc gpu? 
I'm running an i7 sandy bridge with 16gb ram and an EVGA nvidia gtx590--i was having the same problem, and this post actually helped me fix it.
Here's how: open afterburner. turn up fan all the way (don't use dynamic fan--just crank it all the way). Next, close afterburner, making sure you have the icon closed in the taskbar too. Your GPU fan should stay at speed even though Afterburner is now closed.
NOW start Skyrim--it worked for me.