Michel,
I have a few simple queries.

After running the following command
stoch_simul(order=1,irf=0,periods=300) y x ;
I checked the sample size. There are 303 rows (observations) in y and x. Where did the 3 extra observations come from? 
I checked how many observations were used in the file calculating the simulated moments? It drops 101 observations. Is this correct?

There was a file called hpfast.m in Dynare version 3. Where is this file in version 4?
regards,
Maurice