Normally when using the built in settings for a .Net project, user settings are stored in the "settings.settings" project file. During deployment this file is automatically renamed to user.config and is placed in an appication specific folder under the user's profile directory structure. For windows 7 this usually equates to something like:
C:\Users\[username]\AppData\Local\[manufacturer name]\[exe or dll name]_Url_[guid]\[version number]\user.config
However when the DLL is an ESRI extension, the settings get placed into an ESRI folder instead, which I suppose makes sense because that is the actual executable being run. I wasn't able to find any specifics on how this magic happens, but in the event one or more user settings for the extension need to be manually changed (e.g. were corrupted and need to be reset to default) the file can be found at:
If there are a lot of "DefaultDomain_Path_..." folders in C:\Users\MatsonJ\AppData\Local\ESRI\ it might be easier to do a Windows Search for the specific setting instead of using trial and error. Note it *might* be easier since the Windows Search functionality doesn't always seem to work. Also .config files are usually set for index searching only by default so they might need to be set for content search.
Once the correct user.config file is found, simply open the file, make edits, and save. The new setting values will be available the next time ArcMap is opened.