I'm building Matlab 2011b analytic jar but not all toolboxes are being included

I have build scripts that are referencing other toolboxes and the mcc command will build from command prompt on some machines but not from it's matlab GUI IDE environment. Then on another machine it won't build from the command line either. It says it built successfully but only included 1 of 3 toolboxes. I'be used fdep to find out which toolboxes are required and even with those toolbox paths hardcoded into the mcc command they don't get included in the build. I've attached the command line and IDE logs from the machine where the command line works