This is a completely random guess. I don't work with Perl on Windows very often, and have never used it as a service. But maybe (and remember that's a big maybe, i.e. a completely random chance) there is a problem with the shell redirection not working right? Perhaps the environment perl is running in as an NT4 service does not provide enough richness that  < in.txt works right. I wonder if using Open2 or Open3 would be any help. (Do these even work on Windows? Again, this post is full of completely random guesses. I figured some replies would be better than none, if only to give you some ideas of what you can try.)