The shortcut to start Matlab includes in the Target field a -c switch followed by the location of the license file.
So the syntax in the Target field is the path to the executable delimited by quotation marks, then the -c switch, then the path to the license file delimited by quotation marks: "executable path" -c "license path"
ThinApp creates an incorrect entry point from this.
What ThinApp creates is
"executable path" -c "-c "license path"
You can correct this by editing the package.ini file before you begin the 'Build' process.
This is using ThinApp 4.6.1-361923 on Windows 7.