A new server build was installed yesterday. This one is based on the new compiler and development environment that we had to quickly put in place after the old one showed that it was not equal to the task.
So far it is looking better. A lot of the random failures and deadlocks no longer appear to be happening.
I did introduce one change. Ships entering orbit now check their standing to other players, and if warranted, a fight will automatically start. I have personally tested this against the Spartan homeworld and it works just fine.