I have had the exact same issue.
http://forums.civfanatics.com/showthread.php?t=306510
To solve it needed to uninstall mapfinder and reinstall the HOF mod, the only thing i could pin it on was multiple copies of civ running at the same time. Sounds like an issue whilst saving now you come to mention it.
Still struggling to get a good game going, i'm tempted to head down the peaceful PA route, it's just such a drag on slow-athon speed.
This morning when I went to reproduce the error in order to more accurately describe my agony in excruciating detail to Ozbenno... everything worked perfectly.
I don't use mapfinder so I'll make sure to uninstall that though.
Game update: 25 cities in 20ADish and room blocked off for 10 more which I am in the process of settling. My tech slider is set at approximately zero and I am in the process of teching education. This is a rather late date compared to my tiny inca games, but I trust in the teching power of the larger maps in the late game. I aim to crack 11k beakers per turn, not for any particular reason, other than the challenge of it.
This time around I actually managed to grab GLib and Parth. I missed out on the mids which forced me to wipe out the germans and take it from them (their fault for not building spears!).
I was actually intending to leave 4 civs alive for trading purposes, but the germans built the mids and the english owned two of the first three holy cities and kept declaring war on me. I didn't really have a choice did I?
So the remaining leaders are ghandi and lincoln (I think), I have them both at pleased, though some serious negative modifiers are in play. Diplomatically I should be fine.
My massive number of cities means a massive number of courthouses which means plenty of EP to utterly dominate the diplomatic situation.
Two civs alive and unfortunately the one who I didn't share a religion with was the one teching Theology for the AP.
I had to make a decision and decided to burn through that tech myself and chop out the AP. This cost me 8 turns and a bunch of trees that could have gone to another wonder, and I'm still not sure if it was the right decision.
For the first time in a very long time I actually shrined a holy city, I guess these larger maps make it worthwhile. Now I have the AP I'll obviously grab University of Sankore too, just to ensure that the investment in temples/monastaries is worthwhile.
In order to get those turns back I'm going to take a slightly larger risk than normal and tech optics BEFORE setting my Liberalism grab up. The hope is that by popping astro from a hut earlier than normal I can earn those turns back with an earlier than normal observatory in my capital and extra traderoutes from my future colonies (terra map).
I have a much greater number of cottages than normal, due to trying to stay out of the red. That will make the Rep vs US decision tougher towards the end of the game.
At this point I'm still not sure if I'll beat my previous attempt. I've never expanded this recklessly before.