external text interface program will work on R2009b, but not R2012a

Hi all, im trying to run an external program with a fortran text interface through matlab [ie system('program')] on a unix HPC cluster. This works fine on R2009b, but will not work on R2012a. Generally it runs without an error, but no text appears and it does not wait for any input, it just runs and exits. I have tried running it in an xterm window [ie system('xterm -e program')] and it does the same thing. I can't find anything in the release notes to explain this; does anyone know why this might be, and if there is a workaround? I need to use the R2012a version for license reasons.
Cheers, Andy

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Which compiler was used for the fortran code?
Intel 11.1.059
Crackin, cheers Walter, the gfortran workaround from matlab seems to work a treat. Problem solved.

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