Connection refused: Connect

Hi,
Well, yesterday I started running a Hamachi server. It's Bukkit, so for it to be up I use the run.bat rather than the Minecraft_Server. It was working fine until late into yesterday. Though the run.bat was up, nobody could connect. I restarted the run.bat, and restarted my computer. Nothing happened. I closed the run.bat and let it sit overnight. This morning, I open it up and the server is still down. I've tried deleting the run.bat and making a new one, but it doesn't work. When I open up Minecraft_Server to run it, the server goes up. But because it's Minecraft_Server not run.bat, none of the plugins are installed.
Recently before it went down (though nobody was actually online at the time) I was trying to install Citizens and LWC. LWC wouldn't work, Citizens would come up in /help but actually using a command did nothing. Are these linked? Is there a limit to the amount of plugins you can have? I have:
EssentialsGroupManager
iChat (though I'm planning on deleting it since I don't need it)
Essentials
EssentialsSpawn
Factions
WorldEdit
Citizens
LWC

And a couple more essentials that are like LWC. Plus I still want to add an anti-lag and an anti-cheat.
I can give more info upon request. Thanks!