The SysGen v3.1 co-simulation S-function relies on Simulink to keep track of the simulation time. The S-function uses this time to determine how many times the system clock should be stepped during a simulation cycle. If the variable-step solver is used, Simulink eventually looses accuracy in the time it reports, and the time interval continuously gets smaller and smaller. Because of this discrepancy, the Co-Sim S-function will eventually step the clock an incorrect number of cycles, and users will see simulation mismatches as a result.
NOTE: This behavior is not seen if fixed-step solver is used.
This has been fixed in System Generator 3.1 service pack 1