In the Compiler Documentation you can find the following:
"The working directory must be the same as the for the
CTF file to be found or else the directory containing your CTF file must be
on your system path. Therefore, you must start your application from its directory
or else modify your system path. ...Make sure the directory
containing 'myProgram.ctf' is in your dynamic load library path
(PATH on Windows, or LD_LIBRARY_PATH on Linux, for example), or
your application search path (PATH on both Windows and Linux).
Error initializing CTF Archive."
The following error message is displayed when the CTF file is in a different directory, included in the system PATH variable:
The CTF archive does not exist!
When the CTF file is in the same directory as the EXE-file, it works. It also works with different directories in MATLAB R14SP3.