We have an application (A) deployed on JBoss 7.1.1 accepting commands (CQRS,
but only C and Q :) ). A console application (B) is sending a large volume
of commands to create entities in A. Entities in A are validated by Drools
(plain drl files, configured in spring using drools-spring). Most of the
time this works just fine. But sometimes, we get the following exception:

java.lang.LinkageError: loader (instance of
org/drools/rule/JavaDialectRuntimeData$PackageClassLoader): attempted
duplicate class definition for name:
"a/b/c/Rule_person_unique___name_656ee3db19d34e689d95e2d6b2be67b6"
        at java.lang.ClassLoader.defineClass1(Native Method) [rt.jar:1.6.0_30]
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631) [rt.jar:1.6.0_30]
        at java.lang.ClassLoader.defineClass(ClassLoader.java:615) [rt.jar:1.6.0_30]
        at org.drools.rule.JavaDialectRuntimeData$PackageClassLoader.fastFindClass(JavaDialectRuntimeData.java:615) [drools-core-5.4.0.Final.jar:5.4.0.Final]
        at org.drools.util.CompositeClassLoader$CachingLoader.load(CompositeClassLoader.java:254) [knowledge-api-5.4.0.Final.jar:5.4.0.Final]
        at org.drools.util.CompositeClassLoader$CachingLoader.load(CompositeClassLoader.java:237) [knowledge-api-5.4.0.Final.jar:5.4.0.Final]
        at org.drools.util.CompositeClassLoader.loadClass(CompositeClassLoader.java:88) [knowledge-api-5.4.0.Final.jar:5.4.0.Final]
        at java.lang.ClassLoader.loadClass(ClassLoader.java:295) [rt.jar:1.6.0_30]
        at java.lang.ClassLoader.loadClass(ClassLoader.java:247) [rt.jar:1.6.0_30]
        at a.b.c.Rule_person___unique___name_656ee3db19d34e689d95e2d6b2be67b6Eval0InvokerGenerated.evaluate(Unknown Source)
        at a.b.c.Rule_person___unique___name_656ee3db19d34e689d95e2d6b2be67b6Eval0Invoker.evaluate(Unknown Source)
        at org.drools.rule.EvalCondition.isAllowed(EvalCondition.java:114) [drools-core-5.4.0.Final.jar:5.4.0.Final]

Any idea where this is coming from or what's causing this. 

I have never experienced this myself, but after having a quick look at the code I believe this could be a multi-threading problem.
In the abstract class java.lang.ClassLoader the method loadClass(String, boolean) is synchronized, but both org.drools.util.CompositeClassLoader
and org.drools.rule.JavaDialectRuntimeData$PackageClassLoader override this method without the use of "synchronized".

I would suggest you create a JIRA issue for this.