UAC prompts give us a number of possibilities...
First, I note from the UAC prompt that the publisher is unknown, which means the binary is not signed. Keep that factoid in the back of your mind.
Second, the presentation of the UAC prompt could mean a number of things.
1. At its simplest it just means you launched the installer from an unprivileged session and needed a privilege elevation.
2. However, if you launch the installer from the local Administrator account itself (which is disabled, by default, on Win7 systems), and you still get the prompt, it could simply be poor installer design. (Ideally, installers launched from privileged sessions should not further prompt -- unless you have UAC configured to always prompt.)
3. A third thing to consider here, not necessarily related to the prompt, but definitely relevant -- if you Allow the installer, does it present other UI dialogs during the installation? If so, then the question becomes whether the installer supports an unattended/silent installation and what the appropriate command line prompts should be. If it doesn't support unattended/silent installation, then you'll also need to enable the "Can request user input" option on the Advanced options dialog *and* you'll need to have a logged-in user launch the installer. (And, if that's going to happen, it then begs the question of whether you ought just send an email with a UNC link to the installer on the network share.)
Of course, there's another point to be made.... by removing the @ECHO OFF statement, you actually MADE that script become user-interactable, because now the start command needs to be echoed to the Command Prompt window. I'm also questioning the value of the pushd command in this instance. You may find it just as functional to merely call CMD.EXE directly from PackageBoot, and rather than use this string for the Command Line parameters:
start /wait /c %MODULEPATH%\MatLab_R2013a_Win_Install.cmd
simply use this string:
start /wait /c %MODULEPATH%\setup.exe -inputFile %MODULEPATH%\installer_input.txt
and then you can include the installer_input.txt with Additional Files in the package, and you still have a fully-qualified pathname for the setup.exe parameter.
It also allows you do to away with the CMD script completely, which could be part of the UAC issue, as well as a 'user interaction' complication.