The lag is introduced by how they're calculating trade routes--typically when you make a change to a tile (moving a unit onto it, pillaging a road, building a road, etc) the game has to recalculate valid routes based only on adjacent squares. With cities, though, it has to rerun through its calculations for every other coastal city in the world, if you're post-astronomy. Before the patch, I'm guessing they forgot to make the base case in a recursive call very wide-ranging, so it introduced delays quadratic (or possibly exponential--I'd have to dive into the code to see how they implemented it, but the last time I wrote something like that, it was exponential because I'm not a fantastic AI programmer) to the number of cities in the world. On a large map, that number could be big, and when you square it, you end up with a big ol' number and a 2-10 seconds delay while it recalculated every trade route for every other city. In any event, the patch fixed it, for the most part.