Each Time when I do changes on Template I need to RUN SysPrep otherwise when I deploy VM from it duplication of SID is happening .
Any Idea what settings I am missing !!
create a customization specification that you use when you deploy your templates and be sure to check the following option.
then each time you deploy with that spec it will boot once, automatically kick off sysprep, and then reboot.
do not have a template that is part sysprepped ( template has had sysprep run and it was shut down before reboot ), I know of admins that do this and it only leads to problems in the long run.