The issue you describe is an issue of "forward compatibility". To my best knowledge MathWorks trys to ensure that projects from previous versions work with newer versions (backward compatibility), but MathWorks does not ensure that projects from new versions can be used in older versions of SimBiology. You should have gotten a Warning dialog when you tried opening the file with R2012b, didn't you?
Please note that it is possible that you could lose tasks and data associated with the project by opening it in an older version of SimBiology. In case of R2012b and R2013a this kind of issues is unlikely to happen but I would still use the same MATLAB/SimBiology version on both computers.