Hi there!
I have had a similar problem in the last week since 'upgrading' my laptop from Windows XP to Fedora Linux. This was complicated by the fact that NetBeans changed from 6.0 on Windows to 6.1 in Linux, and glassfish went from v2 to v2ur2.
My symptoms were that a request from within NetBeans to start the 'personalDomain' glassfish instance appeared to be ignored by Glassfish for 5 minutes, at which time it would log an 'ASLauncher' message and then start normally. Starting the main 'domain1' instance as 'root' from the unix command prompt worked fine.
After reading this thread I tried your suggestion of switching off the "use ID proxy settings", and the problem has gone away.
Just thought I would add that to the thread. Perhaps the original poster can check that he/she has switched off this setting (and stopped and restarted both NetBeans and GlassFish).
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