Well, here is what we have found out.
Between our windows system and UNIX system a security problem shows up. We don't want to map the UNIX drive so we created a work around. Assuming you already have access to the unix box you can set up a batch file to make the connection, run the program, and then exit. This is what we ended up doing because having the progress program run in the background as a service just took up too much resources. It only needed to check for the existence of files, run a conversion, and then email the results. We then took that batch file (.bat) and created a scheduled task on the server to run every 15 minutes from 8 am to 4:30 pm. Here is the batch code used:
net use z: