Francesco,
Maybe a small model that illustrates the issue would be good. I tried to build up a very simple model according to what you described, but with this model I do not see what you describe. I have attached the model. It has a condition block with two procedure blocks, each one just has a integrator. I ran the simulation with:
y=sim("cond",{time=[0:12]',input=[[0:12]'>6,ones([0:12]')],ialg="RK4",cdelay=1,extend=1})
Carl L
National Instruments
www.ni.com/matrixx