I had this exact same issue when running glassfish v2 from Netbeans 5.5.1 AND Netbeans 6 beta1. It appears that the problem stems from the new Sun Java EE 5 installer putting glassfish in the program files directory. I am running Windows Vista and never bothered to disable the extra security features that constantly prompt me to allow file operations on any "protected" files such as c:\Program Files. By running netbeans as an administrator (right click->run as administrator) the security limitations of a program writing to c:\program files\** are lifted and glassfish will run properly via the netbeans start button.
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