Natural-Selection have released a small update which applies only to users running dedicated servers:
"In response to a number of minor issues with the recent release, we present you with Natural Selection 3.01, a server-only update to 3.0. It fixes the choke issues experienced by the operators of larger servers. On our test servers, we saw performance improvements of more than 20%.
Additionally, we removed an exploit of the updated mapvote system, and fixed a bug that hindered the commander from dropping structures on a specific occasion."
Head over to the site for full details and download links.