I have not been able to figure out how to resolve this bug property so I can't submit a patch to fix it at this time.

Take the standard sample plugin from the source in subprojects\docs\src\samples\customPlugin

As provided the sample plugin will run it's tests correctly using "gradle-build" gradle-1.0-milestone-3 or gradle-1.0-milestone-5.

Now modify the sample (modified example attached) so that the plugin uses a package namespace of "org.example" instead of "org.gradle".

The following files will need the package/namespace references or file paths updated:
build.gradle
usesCustomPlugin.gradle
usesCustomTask.gradle
src\main\groovy\org\gradle\GreetingPlugin.groovy
src\main\groovy\org\gradle\GreetingTask.groovy
src\main\resources\META-INF\gradle-plugins\greeting.properties
src\test\groovy\org\gradle\GreetingPluginTest.groovy
src\test\groovy\org\gradle\GreetingTaskTest.groovy

As modified sample plugin will run it's tests correctly using "gradle-build" gradle-1.0-milestone-3 but with gradle-1.0-milestone-5 you will get the following exception:

Test org.example.GreetingPluginTest FAILED
2 tests completed, 1 failure

FAILURE: Build failed with an exception.

• What went wrong:
  Execution failed for task ':test'.
  Cause: There were failing tests. See the report at C:\customPlugin\build\reports\tests.

org.gradle.api.plugins.PluginInstantiationException: Could not find implementation class 'null' for plugin 'greeting' specified in file:/C:/Users/fstaats/Desktop/customPlugin/build/classes/main/META-INF/gradle-plugins/greeting.properties.
at org.gradle.api.internal.plugins.DefaultPluginRegistry.getTypeForId(DefaultPluginRegistry.java:102)
at org.gradle.api.internal.plugins.DefaultPluginRegistry.getTypeForId(DefaultPluginRegistry.java:76)
at org.gradle.api.internal.plugins.DefaultProjectsPluginContainer.getTypeForId(DefaultProjectsPluginContainer.java:102)
at org.gradle.api.internal.plugins.DefaultProjectsPluginContainer.apply(DefaultProjectsPluginContainer.java:37)
at org.gradle.api.internal.plugins.DefaultObjectConfigurationAction.applyPlugin(DefaultObjectConfigurationAction.java:101)
at org.gradle.api.internal.plugins.DefaultObjectConfigurationAction.access$200(DefaultObjectConfigurationAction.java:32)
at org.gradle.api.internal.plugins.DefaultObjectConfigurationAction$3.run(DefaultObjectConfigurationAction.java:72)
at org.gradle.api.internal.plugins.DefaultObjectConfigurationAction.execute(DefaultObjectConfigurationAction.java:114)
at org.gradle.api.internal.project.AbstractProject.apply(AbstractProject.java:841)
at org.gradle.api.Project$apply.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:40)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:124)
at org.example.GreetingPluginTest.greeterPluginAddsGreetingTaskToProject(GreetingPluginTest.groovy:12)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at org.junit.runners.BlockJUnit4ClassRunner.runNotIgnored(BlockJUnit4ClassRunner.java:79)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:71)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:49)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.execute(JUnitTestClassExecuter.java:51)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassProcessor.processTestClass(JUnitTestClassProcessor.java:63)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:49)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.messaging.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
at org.gradle.messaging.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:75)
at $Proxy3.processTestClass(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.messaging.remote.internal.TypeCastDispatch.dispatch(TypeCastDispatch.java:30)
at org.gradle.messaging.remote.internal.WorkerProtocol.handleIncoming(WorkerProtocol.java:53)
at org.gradle.messaging.remote.internal.WorkerProtocol.handleIncoming(WorkerProtocol.java:31)
at org.gradle.messaging.remote.internal.ProtocolStack$ProtocolStage.handleIncoming(ProtocolStack.java:167)
at org.gradle.messaging.remote.internal.ProtocolStack$BottomStage.handleIncoming(ProtocolStack.java:277)
at org.gradle.messaging.remote.internal.ProtocolStack$BottomConnection$1.run(ProtocolStack.java:299)
at org.gradle.messaging.remote.internal.ProtocolStack$ExecuteRunnable.dispatch(ProtocolStack.java:120)
at org.gradle.messaging.remote.internal.ProtocolStack$ExecuteRunnable.dispatch(ProtocolStack.java:116)
at org.gradle.messaging.dispatch.AsyncDispatch.dispatchMessages(AsyncDispatch.java:132)
at org.gradle.messaging.dispatch.AsyncDispatch.access$000(AsyncDispatch.java:33)
at org.gradle.messaging.dispatch.AsyncDispatch$1.run(AsyncDispatch.java:72)
at org.gradle.messaging.concurrent.DefaultExecutorFactory$StoppableExecutorImpl$1.run(DefaultExecutorFactory.java:64)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.ClassNotFoundException: org.example.GreetingPlugin not found.
at org.gradle.util.MultiParentClassLoader.loadClass(MultiParentClassLoader.java:51)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at org.gradle.api.internal.plugins.DefaultPluginRegistry.getTypeForId(DefaultPluginRegistry.java:100)
... 64 more

The root cause appears to be that line 100 of gradle-1.0-milestone-5\subprojects\core\src\main\groovy\org\gradle\api\internal\plugins\DefaultPluginRegistry.java Now calls a FilteringClassLoader that excludes classes in the project namespace. (Note: the null in the exception is because the the error thrown exception uses the missing class variable (implClass) for the class name instead of the name of the class variable (implClassName) that was looked for... this would also be a minor bug.)