Comparison settings represent a subset of the global preferences used for a particular comparison.
There are two types of preferences in DeltaWalker - global, application-level preferences and session-specific preferences. The global preferences serve as default values for session preferences at the time a new comparison is created.
To change global preferences use the preference pages accessible via DeltaWalker > Preferences...
To change session settings go to File > Comparison Settings... or the comparison's context menu. Finally, the most commonly used comparison settings are exposed via the main and the local toolbars.