Download the latest BIOS update package for your board, which includes updates for the BIOS, Baseboard Mgmt Controller (BMC), and Field Replaceable Unit (FRU) / Sensor Data Record (SDR). Run the FRU/SDR update and select the correct chassis. The SDRs establish the correct fan information for the system.
Make sure the fan cable is installed correctly on the fan headers on the server board. See the quick start guide that came with the server board and chassis for more information.