I saw a post this week by CRM MVP Donna Edwards raising some interesting points about site maps when you upgrade to CRM 2013, here blog post is here
Donna links to an article
Verify new areas are available in the navigation bar
Basically the article above says CRM 2013 has changed the navigation bar and so after you upgrade it might not have added the new navigation areas because it was persevering your old navigation settings.
So what might happen is some of the navigation links will be missing after you upgrade.
Verify whether new areas are available in your upgraded organization
After you upgrade to Microsoft Dynamics CRM 2013, if you have the System Administrator Role you should be able to use the navigation bar to go to the following areas listed in the following table.
|Sales||My Work||What’s New|
|Service||My Work||What’s New|
|Marketing||My Work||What’s New|
|Post Rule Configuration|
if not you will need to manually add them to the site map, instructions on what to do are here, although I would use one of the tools available rather than manually editing the xml