It's not because of FPS Booster. All actions you do (building/bulldozing/moving) are done on the simulation thread and if it is running slow you will experience that behavior (especially when you run 3x speed). Simulation is independend from the main thread that is rendering things so that sort of "lag" is expected but shouldn't take few seconds. Try Broken Nodes Detector mod, maybe something is wrong (a broken node can cause performance issues on simulation thread)

Thanks for the reply. I'll try the mod and see what happens.

Well, finally I had the chance to test the Broken Nodes Detector mod. All it detected was a broken bus line, nothing more, and it still kept the very laggy simulation. So I tried starting a new map and finally it worked correctly.
Perhaps the city was getting to big, after all it was 130,000 pop. But I hope the same issue doesn't repeat in the new city.
Anyway, thanks for the tip. If anything else pops up I'll update the thread.

Check game limits with Watch It, and if you use TM:PE then at the Maintenance tab enable Path-find counter - it will show pathfinding queue length when you open TM:PE menu. If number is too big (depends on CPU 200+ or constantly rising will be the problem) it will slow down simulaiton to help path-finding threads with calculating paths (slowing simulation will reduce number of new path requests).