Instances get incremented when their related dimension has a value set with it in a beacon. For example, when eVar123 gets set with a value, then its eVar123 Instances increments by 1.
So likewise with Tracking Code Instances and Marketing Channel Instances: they increment when new values are set in their respective dimensions. In the case of Marketing Channels, recall that new values can be set when the same visitor browses your website from various traffic sources, even within the same visit. As a result, you can expect differences between Marketing Channel Instances and Tracking Code Instances.
Think about how your visitors arrive at your websites, and that should help you figure out what you're seeing in your report.