I do have the exact same problem, but with a newly created world.
Sysspecs are:
ESXi virtualized environment. Physical specs: 8x Cores (2x Xeon E5602), 24Gb RAM.
Virtual server for MC: 4x cores, 12Gb RAM, Ubuntu Linux x64 (Java heap size 8G max, 4G min), running MC from ramdisk. Pack is Direwolf20.
Current online count is eight players, but I already have 300+ ms in a tick rate delay (using /TPS command). Using ForgeTools "/mobs d" I see - I have 5000+ passive mobs spawned, but I have no idea is it the case, or something else.
"top" command give me approximately "1.20" state, 80% CPU idle (0 - 0.5% wait), 15-20% of RAM free, no swapping.
"java" process using about 130% of CPU, about 15% of memory.
So I just can't think of anything trying to find a source of lag... Could you advise me something pretty please?