Alternatively you can set this programmatically, e.g. in your WorkbenchAdvisor's initialize Method.
PrefUtil.getAPIPreferenceStore().setValue(
IWorkbenchPreferenceConstants.SHOW_INTRO, true);
PrefUtil.saveAPIPrefs();
But since PrefUtil is an internal class this is only recommended if you can't set this property in your xml (e.g. you have an intro which is not based on the Standard Intro page)
PS: The problem you have is that as the intro appears, the preference property you have set via plugin.customization is set to false, and plugin_customization only sets preference store default values, as soon as as any component sets the value, the default value becomes obsolete. With this two-liner you're setting this preference key to true on every startup and the intro will appear.