tomas: you may be able to work on this one as you work on bug #212011...

I tested it under debugger and saw following stack trace:
INFO [org.netbeans.modules.j2ee.deployment.devmodules.api.Deployment]
The module has not been deployed.
See the server log for details.
[catch] at org.netbeans.modules.j2ee.deployment.devmodules.api.Deployment.deploy(Deployment.java:210)
	at org.netbeans.modules.j2ee.ant.Deploy.execute(Deploy.java:111)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor115.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:348)
	at org.apache.tools.ant.Target.execute(Target.java:392)
	at org.apache.tools.ant.Target.performTasks(Target.java:413)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
	at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
	at org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor115.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:348)
	at org.apache.tools.ant.Target.execute(Target.java:392)
	at org.apache.tools.ant.Target.performTasks(Target.java:413)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
	at org.apache.tools.ant.module.bridge.impl.BridgeImpl.run(BridgeImpl.java:283)
	at org.apache.tools.ant.module.run.TargetExecutor.run(TargetExecutor.java:541)
	at org.netbeans.core.execution.RunClassThread.run(RunClassThread.java:153)

Seems to be some kind of race condition. When debugging the target IDE the issue is not visible. Once debugger is disconnected the issue is reproducible on Windows, but so far does not seem to be platform specific.

Created attachment 121192 [details]
patch

This patch seems to work for me. It is too late for me to do additional checks. I'm also not sure the atomic reference is really needed. Perhaps just reordering of listener registration.

As bug seem to be bit random the patch certainly need more testing. Tomasi feel free to test whether this fixes things on your setup.

Created attachment 121205 [details]
updated patch

I think there is one more problem as state set in j2eeserver by the profiler listener is not propagated to common part of GF.

Created attachment 121211 [details]
final working patch

This is the final patch. There is one ugly WA in GF. Please verify and/or comment.

I'm rebuilding NetBeans with this patch but it takes time ...

compile:
    [mkdir] Created dir: D:\tomas\nb72\glassfish.common\build\classes
 [nb-javac] Compiling 112 source files to D:\tomas\nb72\glassfish.common\build\classes
   [repeat] D:\tomas\nb72\glassfish.common\src\org\netbeans\modules\glassfish\common\CommonServerSupport.java:80: cannot find symbol
   [repeat] symbol  : class GlassfishModule3
   [repeat] location: package org.netbeans.modules.glassfish.spi
   [repeat] import org.netbeans.modules.glassfish.spi.GlassfishModule3;
   [repeat]                                          ^
   [repeat] D:\tomas\nb72\glassfish.common\src\org\netbeans\modules\glassfish\common\CommonServerSupport.java:95: cannot find symbol
   [repeat] symbol: class GlassfishModule3
   [repeat] public class CommonServerSupport implements GlassfishModule3, RefreshModulesCookie {
   [repeat]                                             ^
   [repeat] D:\tomas\nb72\glassfish.common\src\org\netbeans\modules\glassfish\common\CommonServerSupport.java:80: cannot find symbol

Created attachment 121217 [details]
correct patch

Ooops. There is missing file in the previous patch. This should work.

Thank you Peter. Problem is resolved also in my environment.
Now it starts glassfish correctly. Please push this fix into repository and close this bug.

Fixed in web-main 74f26d341f9b.

Jirko, please verify. I suppose this should be pushed to 7.2.

Integrated into 'main-golden', will be available in build *201206230002* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
Changeset: http://hg.netbeans.org/main-golden/rev/74f26d341f9b
User: Petr Hejl <phejl@netbeans.org>
Log: #213640 - repeated profiling doesn't work

Verified in dev build 201206250002. Still facing bug 214554.

For sure needs good verification. ;) I didn't know gf codes in detail but I
dind't find anything wrong and the concept looks Ok to me as well.

Pushed to release72 as 9432daf397db.

Integrated into 'releases', will be available in build *201206262201* or newer. Wait for official and publicly available build.
Changeset: http://hg.netbeans.org/releases/rev/9432daf397db
User: Petr Hejl <phejl@netbeans.org>
Log: #213640 - repeated profiling doesn't work

Verified in NetBeans IDE 7.2 RC1 (Build 201206262201).