Problem: SharePoint v3.0 doesn't template default views for anything on the main page. This is stupid and not helpful when you are deploying more then 5 sites. The Toolbar settings do not template either. If you have a custom view in SharePoint save and template the site. then deploy the site the views are there just not selected. Whats the point if you still have to go back and re-select all the views. This is a pain when it's 40 to 50 sites.
Problem: I have also found a bug in the menu system on the left when you setup a template, then deploy, some of the links do not update and stay pointed to the template site.
Attachment: You can see in the attached file that the main links work correctly and go to the correct link these are updated when the template is deployed. However, the option for Project Files is not updated and keeps it's old link. v3 is the site we used to create this template. This has happened on all the deployed sites with this and other templates.
NOTE: I am only using WSS 3.0. this may not apply to MOSS 2007