There is an issue in Dynamics CRM with SiteMap order, there is no way to set the sequence of the SiteMap area items. When importing a few solutions with sitemap changes, if there is a sitemap conflict it will put the sitemap area at the end of the sitemap.

There should be a sort order value that can be set so you have full control over the order of the sitemap areas.

When there is a conflict it just puts the area in the next available so there are inconsistent results over multiple Dynamic CRM deployments