Anytime you convert from one model type to another in MATLAB, there is some accuracy lost due to the numerical accuracy of the computations. You can read more about these in the following link:
For instance, if you do not have a minimal realization of your model in state space, then the conversion may lead to two systems whose behavior is different. Consider finding a minimal realization of your system either by hand or by using MATLAB's "minreal" function. This function eliminates uncontrollable or unobservable states in the state-space models leading to a minimal realization of your system. You can read more about this function here:
