What is the current state of the status LED of the board? Could you please confirm the model of the chassis is being used?
Remember to properly close the side cover of your chassis as this might cause the fan to run at full speed.
If all the settings are the same, the chassis is the same, and the updates were run in the same order as far as the FRU/SDR selections; then, I would suggest opening a case with our Intel Customer Support team to gather the logs of the systems and find out what is causing the fans to run at full speed.
Were you able to check if the side cover is properly mounted? I would probably try the EFI update instead to see if it has the same effect.
If the fans are able to run slow during the BMC update, it is a good sign that the unit should be able to control the fans. You may find the EFI package here. Make sure to select option#3 for the FRUSDR.
If the issue remains, I would recommend gathering a set of logs with our Intel System Information Retrieval Utility.