Doing lots of building I get this quite a bit, pretty sure its tied to all the background scripts needing time to catch up.
To help it do it quicker, if you have an ENB, turn it off for a little while (my default toggle key: scr lk) and look at the ground to get max frame rate.
My understanding is that the scripts are tied to framerate, and for me, the higher frame rate the faster it sorts itself out.
Works to speed up city plan building too.