Here are the steps that I would recommend following, so you can diagnose it more clearly:
- Make a singleplayer game with the exact same modlist you use for the server.
- Try to reproduce the problem in the singleplayer game. If it doesn’t happen, then the server database must have been corrupted in some way.
- If the problem does happen in singleplayer, start taking mods out of the modlist one by one.
- Every time you take a mod out, try to reproduce the problem. When it stops happening, you’ll have a better idea which mod caused it.
This process doesn’t account for the possibility that it isn’t just one mod that causes the problem, but rather a combination of two or more mods. However, I think that should be really rare and I don’t want to suggest trying out all 2048 combinations necessary to figure that out 
4 Likes