No, this issue does not relate to lighting updates. Just placing command blocks causes the lag.
I'm not sure where this issue happens exactly, but for me it happened at Y=238, around X=0, Z=0 (The spawn chunks). It seems to only happen every once a while. I'm not exactly sure how to reproduce this, but if somebody else experiences this, I'd be very happy if they could tell me that.
We need more infiormation to reproduce that.
Can you recreate this issue in a new world ?
If so, please ZIP and attach that world here.