See this thread, particularly reply #5: https://forums.sinsofasolarempire.com/336965
Note that since that since I made that post, they've released one sync bug fix (1.13 for Sins, or beta 2.5 for Entrenchment, since you didn't specify) and have also found one more but we don't have it yet.
Either way, if everyone from your desynching games can send those checksum snapshots after you change those settings, it'll let them know if it's a new bug or same one.
