Compiled Script (moveToNextHole) not executing when run as a service on windows 2012 Server

So I have an interesting problem. I have a matlab script that generates a report using the report generator. When I compile it, it runs fine. I move it over to a windows 2012 server, double click it from the windows interface, it executes fine. However, I have a another application installed as a service on the server, and at certain times that service runs my compiled matlab script. When it runs from the service, it hangs up. Specifically it hangs when the script executes the moveToNextHole command. I have pin pointed it to this line in the code as I sent emails to myself after each line of code.

Does anyone know how to work around this when the compiled matlab code gets executed by a service on a windows 2012 server?

D = Document(fileout,'docx',tempname);

moveToNextHole(D);