Some issues with my Bukkit server.

Hey I've been running a happy bukkit server for around a week now. And yesterday after various bugs kept popping up I sat and updated every single plug-in and the latest version of Bukkit. Now all the bugs I used to get have gone, which is great. But twice in the past 12 hours or so, Bukkit has completely crashed. Given me a load of Java errors and simply locked up. I'm able to save it and stop it when it's in this state, but no one can connect to it. It's a new problem to me, so rather than breaking things further I thought I'd make a post to seek help from people who know what they're talking about more than I.
Also, since i updated the server constantly reports that it can't keep up and it's overloaded? I'm running it on a 2xQuadcore box with 16Gb RAM so surely that should be enough?

Here are the logs before the last crash, at first glance to me it looks like Minecart Mania is causing some problems, It has been incredibly buggy since i started my server, It takes ages for carts to despense from chests when i hit a button, and sometimes when it just ignores the signs next to the track... But it's a pretty vital part of my server due to the ammount of long distance rail-roads.
Anyway, here's the logs, maybe someone can give me some clues as to what i'm doin wrong...

It's rather long as i was off-line when it happened so is just copied everything that looked bad...

Turns out it was too big to post here, so here's the link to a txt file i uploaded...

Thanks in advance.
[MERGETIME="1299938044"][/MERGETIME]
Right. Sorry for the double post/bump. I just thought i'd post an update in the hope of finding some help.
I removed MinecartMania. The crashes seem to have stopped. I'm going to install a bukkit server on my local server to see if I can find what was causing it. Maybe some plugins were conflicting.
Anyway, that's fixed, but still my server reports "Can't keep up did the system time change or the server overload" or some such error. I realise this seems like a RAM issue but I'm running 16gb of ram and the processor in the machine rarely rises above 20% with heavy usage.. So i don't know what this could be. Am I not allocating RAM properly? I don't know. Please help.

 

We need more information.

 

I'm running on Windows Server 2008 RC2.
64x architecture.
Java version 1.6.0_24
I'm not running any wrappers, it's running from a command console on the server.
Bukkit version #531.
the command i use to start the server is:

Code:

@echo off
java -Xmx10240M -Xms1024M -cp BiomeBukkit.jar;craftbukkit.jar org.bukkit.craftbukkit.Main

I'm currently running:
Lockette
chatbukkit and scrapbukkit
BukkitUpdater
BigBroter
dynamic map
KiwiAdmin
General
Permissions
World Edit
World Guard
Multi Homes
iChat
BackupPlugin
milkAdmin
and Minecart Mania but i removed that and the crashes seem to have stopped...

I posed the errors in a txt in the top post.
I have tried removing MinecartMania to stop the crashes and it seems to have fixed it, but my server really requires it to function (long railways and auto-farming). But I'm still getting the "Can't keep up" errors.

Sorry i didn't post this earlier, thanks for putting me right.

Thanks.
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I continued to try to get Minecart Mania to work but to no avail, so I've taken to using Epic Gates plug-in as a temporary fix to get people around the map.

I'd still like to know why it says it's overloaded when the server is more than capable...

 

Either it is minecart mania since it seems to be in most of the errors, try updating the core. Or it could be the problem I am having >.< here