Server Lag, Lower TPS, Dedicated Server

Performance AMD​

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Windows Server 2012​

Hexa-Core Processor Speed 6 Cores x 2.8 GHz​

(3.3 Turbo Core) RAM16 GB DDR3 ECC Hard-disk space 1,000 GB ​

(2 x 1,000 SATA )RAIDSoftware RAID 1​

100Mb/s Uplink​

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I've recently switched to this new host 1&1, this is my first dedicated server; in which reason we decided to use a Windows Server 2012. We've recently had some issues with TPS on my server.​

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The server has 4GB of RAM dedicated to it, as we are hosting it as a hub server. When I type /lag in the game I receive reports of 4-5/20 TPS with only about 20-30 players on. There are no errors coming from the console; we've updated every plugin except for Factions. Every time we try to update Factions it doesn't seem to work. That doesn't matter right now though, I need to understand where my lag is coming from. Even though it says the server has 4TPS and I check the computer only about 15% of the CPU is being used. Is there anyway I can make it so multiple cores are being used to host each server. Could this be the problem I'm having resulting in slow TPS counts?​

 

Maybe a very late response... But have you checked your hard disk activity and the speed of your harddisk? At my servers the harddisk once was a problem. Now it's running on an SSD with no problems at all.
Maybe you also should check out Spigot, it's a slimmed-down Bukkit version (much more efficient).