But my previous GTX260 did not have those 1-2 100% secs (that was way before my current usage pattern).
OK, we may have crossed purposes here. My understanding with NVIDIA cards is as you state above, what you have found with an ATI card looks to be different. How the cards chose to boot and run their fan speeds before and after hand may vary. Still have you actually tried modding the BIOS to look and see if any of the fan speeds are useful?
Which driver are you using? The Catalyst or one of the open source drivers? When are you loading the driver? If you modprobe the driver as soon as you can in the boot process is this a help by reducing the noisy fan time?
Why do you actually need this configuration?