I had a bit of a bad lag spike in Echo Lake during a point in building, too, but it worked itself out. Due to shenanigans, the build started out with the full 6 settlers for the phase 1 city plan. The city plan built the first four houses and work plots no problem then placed the next two plots for work but not for houses, and stuck there for about a half hour. I didn't do anything to fix it, it just kicked back into gear suddenly.
My guess is script lag. I have several other mods that generate a copious amount of scripts that can get SS backed up from time to time. For me, it is usually PackAttack or some combination of that and a few other mods with some minor scripts that just happen to activate simultaneously, and then there are the quest scripts from the main game.
So, with that in mind, what other mods do you have installed and, can you check your save file to see if you have Active Scripts built up?