same here. I think it's Omar's rom „feature“ - my wife's XT890 has untouched ROM and it is not affected by this problem; I've tried both chargers with my phone and both give same issue.
Lags as hell when charging with Samsung 0.7A charger.
Never lags when charging from PC, std USB or high power USB.
Never lags when charging with Motorola charger.
Never lags when charging with in-car charger.