Had a similar problem. Population never decreased, but it stopped going up as well. So, all my cities were stuck on village size. Screenshot included doesn't illustrate too much, except that I've researched the hell outta Farming Bonuses, its many turns in, and my Capital still is only a village.
Also, on a hunch, I tried founding another city near another farming bonus. That brought me up to a total of 2 farming locations. This didn't affect growth at all.

By boeduur at 2009-09-28