I'm afraid I can't seem to narrow down your bug. From what you say it would seem that the city's stopped performing its update per turn, but I couldn't find anywhere in the code paths which would allow that to happen without crashing the entire program. It's probably not to do with Ubuntu, but I'll admit I've only tested it on Linux Mint, so that might be the cause(but it seems near impossible to be the real reason). I'll do some more digging, see if I can't find anything before the next version.
Thanks for the report, though.