1. I’m not 100% sure exactly what is causing the conflict, but it’s most likely another piece of code (html) or a plugin or something. Maybe you’re using a plugin that shows on certain pages? Or maybe you’re adding code in and it’s not showing up right on those specific pages?
2. If you haven’t made any changes to your theme, then I would definitely give the updated version a try to see if you prefer it instead. It’s 1140px wide instead of 960px now (thats what a lot of people wanted)…but you can adjust it to always be 960px if you want. You can check this out for some basic info on the update – http://appfinite.com/topic/optimal-1-3-for-genesis-2-0-html5-is-now-available/
If you decide to keep the version you have, then adding that code should still fix that issue. Just make sure and add in the “clear: both” code exactly as I have it above and you should be fine.