Hey JC, I've not used FMF (fast modelfree) or modelfree yet, but I've downloaded FMF from http://xbeams.chem.yale.edu/~loria/software.php and searched the Perl source code for word 'Error' - nothing like what you have was found.
That means your file is not recognized by the underlying modelfree program. Maybe you could investigate the input file format for modelfree? I hope someone will give a better advice.