Mass Disconnects "Main thread failed to respond after..."

I am getting the below message followed by the server booting everyone online. The server will bring itself back, as it never actually shuts down. I will go a full day without getting it once, then get it three times in an hour. It seems random. This is the only error logged... Ideas? I am clueless. I am on #2586, Beta build of Bukkit. TPS is always 20/20.

Code:

2013-01-02 15:25:06 [WARNING] [Server] The main thread failed to respond after 10 seconds
2013-01-02 15:25:10 [WARNING] [Server] What follows is the stack trace of the main thread
2013-01-02 15:25:10 [WARNING] [Server]    at java.io.FileOutputStream.writeBytes(Native Method)
2013-01-02 15:25:10 [WARNING] [Server]    at java.io.FileOutputStream.write(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.io.BufferedOutputStream.flush(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.io.PrintStream.flush(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.io.FilterOutputStream.flush(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at sun.nio.cs.StreamEncoder.implFlush(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at sun.nio.cs.StreamEncoder.flush(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.io.OutputStreamWriter.flush(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at org.bukkit.craftbukkit.libs.jline.console.ConsoleReader.flush(ConsoleReader.java:707)
2013-01-02 15:25:10 [WARNING] [Server]    at org.bukkit.craftbukkit.v1_4_6.util.TerminalConsoleHandler.flush(TerminalConsoleHandler.java:23)
2013-01-02 15:25:10 [WARNING] [Server]    at java.util.logging.ConsoleHandler.publish(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.util.logging.Logger.log(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.util.logging.Logger.doLog(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.util.logging.Logger.log(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at java.util.logging.Logger.info(Unknown Source)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.PendingConnection.a(PendingConnection.java:138)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.NetworkManager.b(NetworkManager.java:295)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.PendingConnection.c(PendingConnection.java:51)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.DedicatedServerConnectionThread.a(DedicatedServerConnectionThread.java:44)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.DedicatedServerConnection.b(SourceFile:29)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.MinecraftServer.r(MinecraftServer.java:585)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.DedicatedServer.r(DedicatedServer.java:224)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.MinecraftServer.q(MinecraftServer.java:481)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.MinecraftServer.run(MinecraftServer.java:416)
2013-01-02 15:25:10 [WARNING] [Server]    at net.minecraft.server.v1_4_6.ThreadServerApplication.run(SourceFile:849)

Code:

Java                : Oracle Corporation 1.7.0_10 (http://java.oracle.com/)
Operating system    : Windows Server 2012 6.2 (amd64)
Available processors: 8
Free memory        : 1777 MB
Max memory          : 9102 MB
Total memory        : 8277 MB

Code:

WorldEdit            : 14-baf032a
Simple-AutoSave      : 0.2.1
Buycraft              : 4.8
Backup                : 2.1-dev
Vault                : 1.2.18-b229
Backpack              : Unknown
PermissionsEx        : 1.19.5
Multiverse-Core      : 2.5-b652
Questioner            : 0.6
WorldGuard            : 752-548bdb7
boosCooldowns        : 3.1.1
dynmap                : 1.2-1438
iConomy              : 7.0
Register              : 1.8
AuthMe                : 2.7.0b2
DragonTravel          : 1.8.3b
CraftBookCommon      : 1541-520ec0b
HawkEye              : 1.1.0
RateOfXray            : 1.0.12
GoogleThat            : 0.0.1
BKCommonLib          : 1.4
ZavAutoMessager      : 2.1
Votifier              : 1.6
CraftBookCircuits    : 1541-520ec0b
Essentials            : Pre2.9.6.7
HyperConomy          : 0.957
WorldBorder          : 1.6.1
Citizens              : 2.0.6-SNAPSHOT (build 651)
CraftBookMechanisms  : 1541-520ec0b
Towny                : 0.82.0.6
EssentialsSpawn      : Pre2.9.6.7
Multiverse-Portals    : 2.5-b668
Multiverse-Inventories: 2.5-b310
Multiverse-SignPortals: 2.5-b641
EssentialsGeoIP      : Pre2.9.6.7
VanishNoPacket        : 3.14.2
ScriptBlock          : 0.8.7
LWC                  : 4.3.1 (b800-git-MANUAL) (December 26, 2012)
Denizen              : 0.7
Sentry                : 1.2.6b
NoLagg                : 1.89.4
TownyChat            : 0.35
LWC-Economy          : 1.3
Dynmap-Towny          : 0.40

Startup: title Minecraft_Server
java -Xmx10G -Xms6G -jar craftbukkit.jar

 

VPS or physical machine? IO bottleneck?

 

Physical machine. Running in a RAMdisk, cannot see how that would be possible. Network usage is like 1% of capacity. I do have hourly backups to physical disk, I wodner if that could be affecting it...