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After the first one or two hundred turns, the game gets really slow between turns. Up to 5 minutes from one turn to the next, though generally only 2-3.
Please attach a save file (zipped) and the .log files in the directory discussed on this page: http://freeorion.org/index.php/Config.xml
Ideally, make new log files by loading a game and ending turn once such that it takes a long time, then quitting the game.
If files are too big to attach, you can use an upload site, or post them on the forums.
Fixed in subversion, sort of...