Time_wait does not cause conflict. After some time if you check again you'll see all you time_waits have disappeared. In plain language it is one of the state of shutting down the port.
In your script of restart, precede shutdown with start
echo start domain....
start D:\dev\server\bin\startgf.bat
echo stop domain....
call D:\dev\3rdparty\glassfish-v2ur2\glassfish\bin\asadmin.bat stop-domain
exit
use :
echo stop domain....
call D:\dev\3rdparty\glassfish-v2ur2\glassfish\bin\asadmin.bat stop-domain
echo start domain....
start D:\dev\server\bin\startgf.bat
:)
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