I think I've figured out why.
60 players on the server, the server was only using around 2mbps of bandwidth. For the heck of it, I changed netspeed. 30 players rejoined and it was streaming around 8mbps. 4x the data being transferred for 1/2 the number of players. So you'd think the server was being limited by the setting.
But to go even further, I wonder if the same thing is happening to clients. I seriously suggest going into your conf.ini in the 1cSoft folder and doubling it to 20000. After rejoining, I barely got a single pause in 2 hours worth of play. That's on a laptop in a hotel
But I bet I'm on to something. Please try it.