When analyzing a webpage through the Current Document tab, two options affect how or when the analysis is run: on-demand vs. automatically.
When the "Automatically" box is unchecked, analysis is performed on-demand by clicking the "Now" button for each page that you want to analyze. As you click through pages on the website and click the "Now" button for each page, the issues found are compiled on the Reports tab.
Checking the "Automatically" checkbox will turn on the dynamic analysis feature of FireEyes so that it analyzes pages automatically as you click through the website. Typically, it is best to leave the "Automatically" checkbox unchecked unless you intentionally want to analyze every page you view, which will utilize extra system resources.
Go back to: the FireEyes Current Document tab - Overview.