Cannot explain the problem, or why fan 3 claimed to be spinning at 10800 RPM, but glad it is working now after a firmware update.
Strongly suspect there is a fan that was malfunctioning...
I do not recommend to run the miner with only 3 fans it wouldn't be enough to cool down your miner while mining because if the miner overheats you just shorten the lifespan of your hashboard so you better wait for your ordered fans before running the miner again.
And about the RPM it might be just an airflow imbalance as said above having extra fans is a good way to troubleshoot this case.