Okay, looks like two different things going on here. Both are probably related to Matlab's current directory.
!/home/atrac/code case172.jcl
error:- ls: cannot access ./id: No such file or directory
ls: cannot access ./id: No such file or directory
Here, it looks like you're managing to run your code program, but code or the JCL script is looking for a file named id in the current working directory. When you shell out from Matlab, that's going to be Matlab's current directory. Run pwd from the Matlab command prompt to find out where you are. You can probably fix this by using cd in Matlab to move to the directory where the id file actually exists (I'm guessing it's in /home/atrac), and then running code using the same command line. A better fix would be to rewrite code and/or the JCL script to work when run from any path (maybe by using absolute paths), so your cwd doesn't matter.
!gnome-terminal --command "./home/myhome/code case12.jcl"
error: There was an error creating child process for this terminal
Here, the leading "." is probably messing it up, because it's now looking for home/myhome under the current working directory, instead of under the root directory. Try doing !gnome-terminal --command "/home/myhome/code case12.jcl" (without the ".") instead.