Actually I have done this many time for purchased apps. One App in particular Altiris is notorious for doing things like this. Most recently One of thier web plugins wouldn't work, so the admin of the servers came and got me, the plugin worked for him and other admins but no one else, instantly obvious to all of us that it was a permissions issue, but where.
He had called their support. They were trying to figure it out for over a week. To which I fired up filemon on the server and hit the webpage. Sure enough for some dumb reason they were trying to store something in an xml file under App Settings for All Users which of course the people logging in from a web page did not have write permissions too. Unfortunately we had to give them write permissions to this one specific xml file but still why a programmer of a web piece would want you to allow everyone write access to the C drive and then just assume you would give it to them. I haven't checked back with the admins to see if they ever did fix that but I know there were other wacky things they did. Anyway this could have been months for them trying to figure out without filemon. This is definately a good tip for people that might not think about using it in that way, thanks for posting it