Sometimes people need a rough wooing to be friends.
As to the save - I was thinking about this, because I had something happen a little similar on my most recent game with my food/civ goods supply (but I was able to fix it). What happened for me was each pop ending up - thanks to various techs and whatnot - producing a lot more from their given job. So when I had a run of new buildings creating specialist jobs this did two things: it increased my civ good requirement from increased upkeep of specialists and from jobs that use civ goods; it also took pops from worker jobs. Now despite having a nation of over 1000 pops my food surplus was under 100. It took shockingly few pops for that to turn unto a -100 deficit. My goods situation was better because I had a larger surprlus and the effect was therefore more muted, but real. Minerals can also be hit in this fashion, as of course expansion of certain specialist jobs increases mineral demand. Energy I found the most forgiving, but even then the shifting of pops can cause fun and games.
@Tom D. There is no sector limit now, but rather Empire Sprawl. If your sprawl exceeds administrative capacity you start getting increased costs for leaders, tech and traditions. Whilst an annexation will therefore cause some increased energy running costs in the form of leader upkeep, the upkeep cost is relatively mild (as the base upkeep is only 2/energy leader). What it may well do, however, is screw up how everything else interlates together.
