I've had this happen a few times as well, although I mostly had problems getting the log window back in front of the main game window... I've never found a really reliable way to get the windows sorted out properly. Sometimes after you Alt+Tab a few times or select the game in the taskbar it works again, sometimes it doesn't.
It's happened enough times that I automatically disable the 'display log on turn start' when I'm going to switch back and forth a lot. Haven't had any problems since.
I also always use autosave on every turn ever since I first ran into this.
Yeah, I have started auto-saving as well. I still would like to not have to reload my game too much, and would die without the log showing at the start of my turn, haha, so I'll probably just have to learn to be more selective with when I tab out. Ah well, thanks for the help!