I've found that in my test sites I've created, changes to page templates are not propagating as they are supposed to. I'm not sure if this is due to my use of a custom layout template in the page template or if it's a general issue with page templates.
Steps to reproduce:
1) Create a custom layout template in the Liferay SDK
2) Include an embedded portlet in one of the template's regions (I had an embedded Navigation Portlet in mine)
3) Deploy the layout template to your Liferay instance.
4) Create a page template and apply your custom layout template to it
5) Add some other portlets to the other regions in the layout
6) Create a site template and make a page that uses the page template you created
7) View the site template's pages and navigate to the page you created in step 6
8) You should see that the page only shows the embedded portlet and none of the other content you added to the page template in step 5
9) Create a new site, or use a site you've already created
10) Add a new page to the site that is based on the page template
11) View the site's pages and navigate to the new page; as with step 8, you should see that the page only shows the embedded portlet and none of the other content added to the page template in step 5
This is a pretty major bug and should be fixed ASAP, as creating layouts with embedded portlets is not an uncommon practice. If the correct practice going forward with page templates should be to just have the custom layout template with nothing embedded and then to add whatever portlets are needed, this should be noted in the online documentation so that developers know they need to revise their existing layout template projects.
In my case, the embedded portlet is there so that site admins can easily create pages that have a second nav menu that shows the current level of navigation links in addition to having the main menu displayed in the theme. This lets a user see the "third level" and lower links that are not normally shown in the site navigation.