So this is an issue we have literally been having for years. I'm not sure if it's something integral to Rust, or something specific to our setup, but this has been plaguing us for quite a long time. I plan to fire up a test server with a copy of ours so that I can finally try and figure out why that keeps happenning. Stay tuned for updates.
Update: This is still broken. I am still testing.
Update: I added a new plugin called Disbanded Teams Restore that specifically addresses the issue with teams resetting on server reboots. Now it creates a persistent mini database with all the teams info that force-restores after every reboot. This should hopefully solve the issue.
Update: The Disbandanded Teams Restore did nothing to solve our problem. However one of our community members, Death, suggested restarting the server through RCON as opposed to LinuxGSM, and that seems to be working. Stay tuned for more (potentially disappointing) updates.