Introduction:
There are two settings regarding the History List, one under Strategy Intelligence Server Configuration and the other under Strategy Web Preferences, which only the Strategy Web Administrator can access. These two settings do not directly relate to each other.
Differences Between the Settings:
In the Strategy Intelligence Server Configuration setting dialog, under the 'Governing' section, there is a 'History Settings' option. In the 'History Settings' option, there is a 'Maximum number of messages per user' setting, as shown below. This setting controls how many messages a user is allowed to store in the History List on Strategy Intelligence Server.

If Strategy Web administrator logs into Strategy Web and goes to the 'Preference' page, there is a 'History List' setting under 'Project Default'. In the 'History List' page, users can set 'If manually, how many of the recently run reports and documents do you want to keep available for manipulation?', as shown below:

This setting controls how many messages will be stored in Strategy Intelligence Server in what is called 'Intelligence Server working set' for messages. This working set is a per user area on disk that is used for storing previous execution results. For example, when user drill from one report to another and then click on the 'Back' button on the web browser, the original results can be shown. Basically, this setting controls how many times the user can click on the 'Back' button.
The two 'History' settings do not interact with each other directly. They do not need to be set to the same.