I was a little intimidated to try to sift an 1800+ post bug thread, but I'm a newcomer to the community patch and loving it. Each of my games however (under 5/2, 5/6 and now 5/9) have come to a premature end due to this same end of turn issue.
Googling the issue wasn't much help, it was kind of a "well it happens sometimes, tough luck." I'd never experienced this though prior to trying CP and only the modules listed in the main post about how to put together the small list of files.
If I'm hearing that enabling logging and sending a lua log file is of development assistance, I could see my way clear to that.
Great work though what I've seen, giving the game a new lease on life for me, cheers for that.