I would assume it might be one of two things maybe? How big did you make the trench? If it's too big it might reduce the velocity of the fuel/air mix. Or it could because the engine is intaking even more fuel now since the piston doesn't block off the intake anymore. Maybe try re-jetting?
Also do you have both a trenched port AND a windowed piston? I'm not sure but I don't think both would work at the same time.
Looked online and someone had a similar problem:
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