I am aware there are a few posts with this topic, and I have used the nav rejg file -
I have two custom post types in my menu and on the first one after applying the rejig it works, but on the second one, again I have two active highlights.
the item in question can be viewed here. They are both CPTs but the first one (gaming) is now behaving properly.
All I actually did was download the new themes replace the files in the lib file - but it could have been a cache issue - its working beautifully now. - thanks for fixing, it was driving me insane on my own site CreativJam - but I will be able to reslove it now. Other than that though, LOVE roots, it is so great to work with!