Server crashing and bad packet id 128

Hello,
I am having some issues since 1.4.
During my scheduled reboots the server keeps hanging at closing listening thread.
2012-11-09 10:33:36 [WARNING] DSCT: Socket closed
2012-11-09 10:33:36 [INFO] Closing listening thread

Furthermore once in a while all the players on my Survival world get kicked with Bad packet ID 128, all players on OTHER worlds, like Factions, are not getting kicked. Just the players on the survival world.
To fix this I have to reboot the server, and then we are fine. I checked the server logs and it does not show any console error when all players get kicked. It just shows like this

Currently running:
WorldEdit/Guard, WorldBorder, Vault, Votifier, uHome, Stargate, ReportRTS, PermissionsEx, Nocheat+, Mv-Core, Mv-Inventories, LogBlock, Jail, iConomy, Herochat, Factions, Essentials, Dynmap, Duties, Chestshop, Cashflow.

Quad core i7 with 16 gigs of ram. The minecraft server runs in a ramdisk.

edit: extra info
Running JDK 7u9, Centos 6. Server was running fine on 1.3.2, the 1.4 vanilla tempmap, and the 1.4 bukkit testserver.

edit: even moar info
Running build 2457 from dl.bukkit.org

Any idea what might be causing it?

Regards,
Nordic

https://bukkit.atlassian.net/browse/BUKKIT-2808
Issue is in Minecraft itself.

EDIT by Moderator: merged posts, please use the edit button instead of double posting.