City growth will lead almost immediately to a desync, if client and server did not use the same compiler and platform. The random counter is ok, so somehow in the implementation of the city rules rdwr a client/server different settings appears.
Client MSVC/server Mingw is easy to reproduce this.
EDIT: rules are identcally, but growth is compiler/backend dependent.
Could not reproduce this with executable from the nightly-page (compiled with mingw?) and my own compilation with MSVS.
Did you use the "found new city" or "increase city population" tool? Both start with exactly the same random counter but get different results.
EDIT: It seems undefine debug or define optimize will do the difference. Therefore in some ****erting or DBG_MESSAGE the random generator is called or an ****ert is changing the game state. I will start looking for it :(