That is what we ran into. We had a client that uses an external reservation system that is loaded in an iframe, but we noticed that even if the iframe loaded the correct page, the screen would flicker and the wrong page would suddenly appear. After much gnashing of teeth, what we finally realized is that we had a Google Analytics script in the code that was pushing a URL to the iframe after the page loaded. The script had the wrong URL. So even though the page would first load with the correct page in the iframe (for just a split second), the script would then fire, replacing the correct page with the wrong page.
The lesson? If you use iframes or any similar technology, be very careful of any scripts that might possibly be changing things without you realizing it.