Publishing sites never allow you to save the site as template to be used in the sub site creation.
to allow this, you need to switch the publishing feature off -> save the teplate -> swtch on oagain!
or else you can append the following URL to force the publishing site to get the site template property.
http://your publishing site name/_Layouts/AreaTemplateSettings.aspx.
Some times the templates created by following the above logic will go weird! Even if you save the template from SharePoint Designer it will go wild and do strange things!
Then you should create site definitions (..\web server extensions\12\template\SiteTemplates) .