This will happen if the PIP filter isn't set sufficiently higher then the rev limiter 1 and 2 scalers. If the engine accelerates past the PIP filter limit, the software defaults to a mode where it drops every other cylinder in the firing order until EEC is reset with a key-off/key-on cycle. I've seen this happen on B9B and X2J EEC's. Who programmed your LPM?
I usually set the PIP filter several hundred RPM higher then rev limiter 1 and 2, but it should depend on how quickly the engine can accelerate. If the engine is supercharged, and/or has a light flywheel, it can accelerate more quickly, so its good to give yourself a few hundred more RPM to the PIP filter.
I'm not sure why the engine calibrators at Ford did this. Perhaps it was meant to be a subtle reminder that you've pushed past what they considered a sane rev imit.