Google Analytics (GA) sometimes has problems tracking within iFrames. This problem happens when the iFrame content is served from a domain that is different than the domain in the address bar. Websites that use a partner site for checkouts or a 3rd party for their shopping cart are often battling these issues. There are much more graceful alternatives to using iFrames, but sometimes resources limit your options, and you need to have visibility into these iFrame content pages.
This security issue isn’t exclusive to GA. Browsers are trying to protect users from XSS (cross site scripting) vulnerabilities, so they throw security warnings and/or stop scripts from running on the iFrame page. In this scenario, the default security settings on most browsers are enough to prevent the Google Analytics tracking code from successfully firing off the image request to the GA servers, but each visitor has the ability to easily change those settings. Keep this in mind when digging into the reports to debug this problem. Just because you see all browsers represented in the reports does not mean that you don’t have a tracking problem. Those visitors could have relaxed security settings.
There are a few workarounds for dealing with this security situation that will help to capture a lot more traffic. One workaround involves the use of Adobe Flash.