IReferenceClock refClock = (IReferenceClock) new SystemClock();
The code just does a different thing. This is system clock being set to you don't show what exactly... Instead, you want to take filter's clock and set it as filter graph clock like this:
IReferenceClock refClock = myFilter as IReferenceClock;
IMediaFilter mediaFilter = filterGraph as IMediaFilter;
mediaFilter.SetSyncSource(refClock);