This might be a bug within Bootstrap itself, but I'm still interested to see if anyone can come up with a fix or at least some help.
To jump straight to the issue, open this jsfiddle in Safari and start to scroll down the page: http://jsfiddle.net/davereed362205122/8bZxb/2/
The scenario:
I have a two column page setup with a right column menu and the following div:
<div class="col-md-push-9 col-md-3">
(The menu needs to show up at the top on mobile devices, hence the push)
Within that div is the affix menu:
<div id="affix-menu" data-spy="affix" >
The main content area is within a div like this:
<div class="col-md-9 col-md-pull-3">
Everything works really well in Firefox and Chrome, but for some reason in Safari the affix portion does not stay confined to the div and overlaps the main content. Taking a look at Bootstrap's own site (http://getbootstrap.com/javascript/#affix), it appears they don't use any push or pulls for their divs, so the menu simply shows up at the bottom in mobile. I'm hoping I don't have to revert to this...