My SiR had the same problem - you could see a big lag-spike in the dyno runs when the VTEC cut in. Would you believe that the solution was a change in fuels? I used to run Shell Optimax (bear with me on brand names, I live on the other side of the world remember) 98 Octane in it but found that BP Ultimate 98 octane was smoother and gave a bit more grunt as well as a different tone to the engine on revs. The lag/spike disappeared after 2 tanks.
Maybe (very possibly) the fuel you are running doesn't suit the motor? It's only a guess though. Try dropping some octane booster in to see.