The Problem: In iOS/mobile Safari, When you have a fixed position nav bar on a page (like this site), once you click a button inside the fixed element, it renders the entire nav bar unclickable. The only way to get it working again is to physically scroll the page with your finger. The buttons react by becoming usable again.
My Solution: Add a significant height to the containing div just before animating to your target page. On complete of that animation, remove the height. I was so relieved to have solved this problem (hacked, worked around), that I posted it on here on stackoverflow.com. Since then, people have emailed to thank me, as well as ask me to help them implement on their sites. If I haven't responded to your email I'M SORRY! I just had a baby and launched a couple of sites. 2012 has been a crazy year.