I contacted my host, and they didn't have much to say: "No, we don't make any changes to the mod_rewrite." They then instructed me to deactivate WordFence.
After installing 5.1.2, I noted that the performance settings were turned off. 24 hours later, all my permalinks were broken again. I've deactivated WordFence now and reset my permalinks.
I don't know if this will help, but here's what I have installed and active:
Akismet
Dagon Design Form Mailer
Disable New User Email Notifications
Disable Trackbacks
Disqus Comment System
FD Feedburner Plugin
Mail on Update
WordPress Database Backup
WordPress Mobile Edition