In your system, is it giving you more lift, duration, or both? Some VVT systems may also only affect camshaft advance. Perhaps, when your VVT switches over, it's going to a cam profile/timing that promotes volumetric efficiency at substantially higher RPM/throttle than you're giving it. That would mean that, because the charge in your intake system doesn't have the ramming inertia to keep filling the cylinder when the intake valve closes after BDC, it's acting more like an "Atkinson" than it was at the mild profile. If you think about it, the cam timing that Toyota calls "Atkinson" in the Prius, sounds a lot like what they use in, say, pro-stock, where they use the long duration and late closure to trap more charge at high RPM. Your engine may be trying to give you power but accidentally giving you economy in this way.
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