Hi,
I think there is an issue when you are building the file paths. You might be creating string arrays instead of combining the strings together to form a single string. Try using strcat to combine strings. Use fullfile to build file paths.
fem_directory = strcat(hypdir, '\FEM_Results');
fem_filename = strcat('CRM_SOL144_', num2str(fuelval(i)), '_new.bdf');
f06_filename = strcat('CRM_SOL144_', num2str(fuelval(i)), '_new.f06');
fem_path = fullfile(fem_directory, fem_filename);
f06_path = fullfile(fem_directory, f06_filename);
oProject.Rundecks.Add(fem_path, f06_path);
-Ryan