Sorry for the late reply everyone. I came home last night and crashed... had a long one today. :( I tried prepending "quit |" to the command, but that isn't working so well. It runs the program, but without the proper arguments. Not sure why, but maybe I could goof around with it.

Anyways, there are some good ideas here. I will play around a bit more after the weekend and try again. The other option is to recompile the program and not have it loop (waiting for more input). I have the source, but I'm about as good as C as I am at administering dental work.