Map Wipe, Error Loading Plugins

Alright so on my server a lot of shit has been happening. First of all, when I start the server I sometimes get some errors about the plugin jar zips not being possible to open. When I take those faulty jars out and replace them they work again until like 2 restarts later where they go back to giving me the error.

http://pastie.org/2262647

This is an example of the error:

Code:

2011-07-21 22:52:42 [INFO] This server is running Craftbukkit version git-Bukkit-0.0.0-945-g73697a4-b1000jnks (MC: 1.7.3)
2011-07-21 22:52:42 [SEVERE] Could not load 'plugins\HeroicDeath.jar' in folder 'plugins':
java.util.zip.ZipException: error in opening zip file
    at java.util.zip.ZipFile.open(Native Method)
    at java.util.zip.ZipFile.<init>(Unknown Source)
    at java.util.jar.JarFile.<init>(Unknown Source)
    at java.util.jar.JarFile.<init>(Unknown Source)
    at org.bukkit.plugin.java.JavaPluginLoader.loadPlugin(JavaPluginLoader.java:60)
    at org.bukkit.plugin.SimplePluginManager.loadPlugin(SimplePluginManager.java:207)
    at org.bukkit.plugin.SimplePluginManager.loadPlugins(SimplePluginManager.java:130)
    at org.bukkit.craftbukkit.CraftServer.loadPlugins(CraftServer.java:128)
    at org.bukkit.craftbukkit.CraftServer.<init>(CraftServer.java:97)
    at net.minecraft.server.ServerConfigurationManager.<init>(ServerConfigurationManager.java:51)
    at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:132)
    at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:335)
    at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)

Also, whenever we crash the map just wipes. It goes back to how it originally was with the seed. We have no idea how this happens as we save regularly.

Is this an issue with the permissions on my server? I am using the Root user to put all these in and do all the server shit. This is on CentOS.