I'm having the same problems using the latest Fan Xpert from the AI Suite posted on 2012.04.10. Running Win7x64 on an ASUS P8Z77 WS.
I just gave up on the software. Can't get it to reactivate a fan profile automatically and has no explicit setting for a default. If you configure a Manual fan profile in the BIOS, you are just as well off. Realistically, you don't need a whole curve to control the fan.
All you really need to do is this:
When you are pounding the heck out of your CPU, run the fan at x%.
All other times, run the fan at y%.
Make x=100 and y=50. Done.
For the temperature thresholds for use in the BIOS fan control, don't use the core temps in RealTemp. The BIOS uses a different temp. If you run AIDA64, it is what is called the "CPU" temp. It's about 20*C lower than the cores. So if you use RealTemp to pick your thresholds, you would probably never hit the upper threshold for the higher duty cycle.