With it being referred to as the system fan, there's a good chance it means the fan for the motherboards chipset. I started to get a similar error as my chipset fan was dying. The fan appeared to be running fine when you looked at it, but it was running between 800 and 1400rpm and should have been at 6000rpm.
I initially thought of contacting ASUS for a replacement fan, but then read that this was a common issue with the fans supplied for the board that I have....It's an A8N SLI SE. I bought an "aftermarket" 40mm fan and rigged it to fit. Only 5000 instead of 6000rpm on the new one, but the chipset is now 6 degrees C cooler than with the stock fan. Oh, and the blue LED in the fan is awfully pretty too.