We are currently customizing a site for a customer, and while doing it, our top navigation bar suddenly stopped highlighting currently selected sites.
The solution to my problem was simple: we modified top navigation manually and added some additional links to sites. If you are adding links to a subsite, it must be formated like this: “/site”. Do not use “/site/default.aspx” because this will cause the problem mentioned above.
If you have ever worked with top navigation bar on a large site, you probably noticed that it has some limitations. I personally like to use Site Navigation Tree Web Part by KwizCom. For complex scenarios you might also consider Telerik controls.