I am a little confused? What do you mean it works at lower frequency? One possible cause could be the implementation errors in FIR/IIR approximation. As i understand, Simulink is a time domain simulation tool, so the filter block must be doing some FIR/IIR for the time domain response. now filters in time domain are designed in respect to sampling frequencies. If your sampling frequency is too high, FIR/IIR implementation might struggle to get a good time domain response.
My response above is acually based on guess work. Without looking at your setup, its actually very difficult to figure out what might be the problem.