ok guys, here is how it works.
The embedded controller is an extra cpu on the mobo from the Renesas (formerly Hitachi) H8S family that runs with a clock speed of 10 MHz. The purpose of this cpu is that it handles the keyboard, touchpad, PS2 connector, batteries, temp sensor and fans. So it isnt really a "keyboard bios" but a "embedded controller firmware". This design is actually quite clever (and a must), because it not only relieves the cpu from doing this, but it is a safety because it handles these important things like fan control and control battery charge even when the main cpu is in standby. The drawback is naturally that the control is hidden away from the main cpu and therefore also the user. Thats why no programs like motherboard monitor can read the temp sensor. So what I did in my temp sensoring program was to communicate directly with the EC. However, in order to control the fan speeds I have to dig even deeper. I have to actually reprogram the EC firmware. This is not a thing to do for the fainthearted, but I know what I'm doing. I dont have a 5680 so I havent flashed this updated firmware, the latest for the 5660 is 1.00.16 which is the one I'm modifying. And yes, I'm sure it returns the Ctrl and Fn keys to their original positions.