As of v4.1, all resources are embedded into GleamTech.FileVista.dll. However it's possible to override embedded resources by putting the customized versions under FileVista\App_GlobalResources folder.
Please first download
Resource files for FileVista v4.1.
For instance, if you want to customize the fileultimate.js file, then copy App_GlobalResources\GleamTech.FileVista\(GleamTech.FileUltimate)\scripts\fileultimate.js file from the above zip file to the corresponding location under your FileVista folder (App_GlobalResources\GleamTech.FileVista\(GleamTech.FileUltimate)\scripts\). Then edit this file to apply your changes. Whenever you do a change under FileVista\App_GlobalResources, ASP.NET engine should restart the application so changes will be detected automatically. If changes are not detected, you can force by recycle the app-pool or touch the web.config (open and save).
For your specific case, edit fileultimate.js and go to line 263:
treeNode.childNodes[0].select();
Comment out this line like this:
//treeNode.childNodes[0].select();
Save the file and refresh FileVista in the browser. You should see that the root folder is not expanded by default.