Hi
All the upgrade docs can be found in
http://www.cisco.com/c/en/us/support/servers-unified-computing/ucs-manager/products-installation-guides-list.html
I don't see any reason why you could not do the upgrade in one step.
I recommend you to open a proactive TAC case, and submit the show tech files.
Problem Subcategory: UCS-B Upgrade
Problem Type: Configuration Assistance
Software Version: 2.1
Problem Details: Firmware Upgrade 2.1 to 3.1 please check for any bugs and caveats