Further evidence (I hope this helps someone solve the problem):

1. 2016b works in NONE of the emacs terminals: shell, term or e-shell.
2. 2016b works fine (even with -nodesktop) from Xquartz's xterm or OSX's
terminal
3. 2016a works fine in emacs
4. Running diff on the java directories (where the potentially offending
files reside) shows NO difference between 2016a and 2016b!
    $ diff -ur /Applications/MATLAB_R2016b.app/sys/java
/Applications/MATLAB_R2016a.app/sys/java

This might not be a Java issue.

On Thu, Nov 10, 2016 at 7:37 PM, Peter Mao <peter....@gmail.com> wrote:

> Yes, I'm seeing this problem, too.  Mathworks won't touch it, as it does
> seem to be a real third party issue with Emacs.
>
> I'm having the problem with OSX 10.12 and Emacs 25.1.1, although it was
> also present with my previous emacs (24.5?).
>
> I checked the environment variables, and the only thing I see
> significantly different is that emacs shell reports as TERM=dumb, while the
> Xquartz one is TERM=xterm and apple's terminal is TERM=xterm-256color.
>
> In all cases, the actual shell is /bin/bash.  I'm guessing this has
> something to do with how emacs is setting up the shell, but I can't figure
> out what the issue is, exactly.  May be time to cross post to emacs
> developers.
>
> Peter
>
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