How can I set the desktop shortcut "Start In" directory created by Matlab 2014b deploytool to the installation directory?

I have used Matlab's (2014b) Application Compiler to compile a Windows executable for my Matlab/Java project. I require a static java library path for the executable so a file called javalibrarypath.txt with a dot ('.') is deployed with the exe in the application directory. Everything works when I double-click on the exe from within the directory. The problem arises when I double click on the shortcut on the desktop created by the compiler (when installing). By default, the short cut does not start in the same directory as the exe (the "Start In" directory is blank). Therefore the Java static path is not set. Is there a way to specify the "Start In" directory to the applications installation directory if the user wants the shortcut automatically, or do I have to have the user install the software and change it manually?

[Joe Kelly]

I am having a very similar issue with deploytool in 2015b. The tool GUI doesn't appear to allow the "start in" parameter to be set anywhere, so I find that I need to create my own shortcut after installation since the one in the start menu fails.