We bought S2400GP2 motherboard and installed it in SC5650UP chassis, I connected fans to SYS_FAN 1 and SYS_FAN 7 and neither of them won't slow down. They are both running at 100% speed all time. Where could I find step by step instructions to solve this loud problem?
I don't think it's a correct combination... SC5650UP is not designed to use with S2400GP. Instead, you should use a P4000M chassis. See Chassis Compatibility.
Anyway, you can try to run FRUSDR update again, select "Other chassis" and select correct fan headers.