I modify our Pro/Intralink batch file with something like copy x:\ptc\proe2001\config.pro c:\proe-loadpoint\text as well as my menu def.pro and color.map files so that each time they fire up the Intralink app. manager they get the latest copy of these files. Hope this helps.
I use a batch file that sits in everyones start up directory, so it runs everytime they log on. It trys to load into very possible place ProE may be installed, if the place doesn't exisit it just skips it: