If you make a fan profile, it should apply as soon as windows boots up. Sorry my earlier posting I was half awake(got to stop doing that).
If it doesn't then clearly there is an issue, Unwinder is the creator of AB. He also supports AB in the forums @guruof3D, link. If you post he is more then happy to help you.
http://forums.guru3d.com/forumdisplay.php?f=55
True. Fan profile creation and implementation was my first reason for needing something like Afterburner; the second reason is to Overclock the GPUs.
But the problem -- as I started this thread -- was that the gfx cards in SLI don't return to their power-saving clock levels at boot time. The are supposed to downclock to 135/162. It appears that re-installing all of the Nvidia drivers "clean" solves the problem; installing Afterburner resurrects it. Whether this is connected to the fan-profile, I cannot say. But as you state, the fan-profile should be effective at windows startup, even if the AFterburner program and interface aren't loaded at startup.
We went through all the possible things that cause this to happen. It just doesn't happen when I omit re-installing Afterburner. Nor, even with Afterburner, does it happen with a single graphics card. Nor does it happen with both graphics cards and SLI disabled. It only happens at reboot, with SLI enabled, and whatever Afterburner does in the background even though it isn't visibly "running" at startup.
I'm wondering what would happen if Ai Suite (for its fan-control and monitoring) isn't part of the startup equation. I think with AI suite Fan-Xpert, you only need it to create the fan profile and it is implemented in BIOS. I could suspect some interference between Ai Suite and Afterburner. We may have overlooked this as a possible system detail of others who have the same problem. It seems that they all use Afterburner. MAYBE they all use Win 7, but that may not be a key factor.
There are probably some loose ends I need to explore about this, before I can feel comfortable using Afterburner again.