Apologies if this is not the right place to post this issue, but I couldn't find a better place!
This problem was originally posted to the matlab.el project on SourceForge. In summary, the latest version of Matlab crashes when started from "shell" or "term" within emacs (I haven't tried e-shell yet, but I can check it tomorrow morning). The program starts up without any issues either from the X11 terminal or OSX's terminal. In my case, it's always using /bin/bash.
The problem appears to be some sort of Java or JRE issue, but I can't imagine how running /bin/bash from within emacs would trigger such an error.