Is the menu in an editable region? If so, then this is exactly what should have happened. The only changes that propagate from Template to child are changes to non-editable regions. We can tell for sure what is happening if you would post a link to one of your child pages so that we can examine the code.
Also, the original template was created using version CS5.5, is that a factor?
No, definitely not.
I'll just add that having your menu/navigation element within an editable region is a VERY BAD IDEA. Just saying....
Of all the content on the page, the very last thing you'd want in an editable region is your menu. Why? Because you definitely do not want to maintain links individually on every page in the site!
Let's see your child page so we can make some face-saving suggestions for you....