Ah yes, I have had a similar problem in the past as well and it may be the same thing.  It sounds like your path is not getting set correctly when MATLAB calls unix() to invoke the bash shell - see http://www.mathworks.com/matlabcentral/n...
where you have to edit the matlab startup file to contain:

export PATH=$PATH:/usr/local/desiredpath

where /usr/local/desiredpath is your path to AFNI's 3dcopy and all other afni tools.  Before trying this however, run !echo $PATH and see if it contains the AFNI directories.  It probably won't given your unix() string gives command not found, but good idea to check first.
Erik