Well, mike was right about deadlocks.

Bukkit-Patches/0004-Make-the-plugin-class-loader-thread-safe.patch

@@ -1,14 +1,14 @@
-From a62dabb02fe7405059ceb42495ed5dbc9704c1ea Mon Sep 17 00:00:00 2001
+From e713a9083b0802334d046915c9f1995326e8956c Mon Sep 17 00:00:00 2001
 From: snowleo <schneeleo@gmail.com>
 Date: Wed, 17 Oct 2012 22:30:45 +0200
 Subject: [PATCH] Make the plugin class loader thread safe
 
 ---
- .../org/bukkit/plugin/java/JavaPluginLoader.java    | 21 ++++++++++++---------
- 1 file changed, 12 insertions(+), 9 deletions(-)
+ src/main/java/org/bukkit/plugin/java/JavaPluginLoader.java | 5 +++--
+ 1 file changed, 3 insertions(+), 2 deletions(-)
 
 diff --git a/src/main/java/org/bukkit/plugin/java/JavaPluginLoader.java b/src/main/java/org/bukkit/plugin/java/JavaPluginLoader.java
-index 10fc26a..f9a09ef 100644
+index 10fc26a..4dca063 100644
 --- a/src/main/java/org/bukkit/plugin/java/JavaPluginLoader.java
 +++ b/src/main/java/org/bukkit/plugin/java/JavaPluginLoader.java
 @@ -45,6 +45,7 @@ import org.bukkit.plugin.UnknownDependencyException;
@@ -36,30 +36,6 @@ index 10fc26a..f9a09ef 100644
      /**
       * @deprecated Internal field that wasn't intended to be exposed
       */
-@@ -293,14 +294,16 @@ public class JavaPluginLoader implements PluginLoader {
-         if (cachedClass != null) {
-             return cachedClass;
-         } else {
--            for (String current : loaders0.keySet()) {
--                PluginClassLoader loader = loaders0.get(current);
-+            synchronized (loaders) {
-+                for (String current : loaders0.keySet()) {
-+                    PluginClassLoader loader = loaders0.get(current);
- 
--                try {
--                    cachedClass = loader.extended ? loader.findClass(name, false) : loader.findClass0(name, false); // Don't warn on deprecation, but maintain overridability
--                } catch (ClassNotFoundException cnfe) {}
--                if (cachedClass != null) {
--                    return cachedClass;
-+                    try {
-+                        cachedClass = loader.extended ? loader.findClass(name, false) : loader.findClass0(name, false); // Don't warn on deprecation, but maintain overridability
-+                    } catch (ClassNotFoundException cnfe) {}
-+                    if (cachedClass != null) {
-+                        return cachedClass;
-+                    }
-                 }
-             }
-         }
 -- 
 1.8.1-rc2