Should it be necessary to change a setting that ArcMapNav uses, you can do that by directly editing the user.config file which is located in a directory such as this:

C:\Documents and Settings\mccann\Local Settings\Application Data\ESRI\DefaultDomain_Path_pz0lsv5r40zaegw4she55pczc5ncbj1k\9.3.1.1850

(Replace 'mccann' with the appropriate login, the DefaultDomain_Path_xxxxxx folder may be a different name, and the final subdirectory will depend on the version of ArcMap being used.)