There is a maximum number of pbos the server will load between the vanilla game pbo and any addon pbos. When more than a certain number of pbos are loaded the server will not allow any clients to join. This makes it problematic to run a server with many mods. To the best of my knowledge this is not an operating system issue as I have already raised the operating system imposed limits.
ulimit -Hn
10240
ulimit -Sn
10240