We successfully resolved our issues with the following steps:
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Cleaned out the server database file of any lingering mod-controller calls to mods we had uninstalled, and any extra remaining files. We noticed people who were freezing were getting flooded with errors suddenly from mods we’d long uninstalled, this resolved some issues immediately.
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Made sure everyone was no longer attempting to connect with the auto-generated modlist that server connections can generate. Everyone had to have their manual modlist.txt in their Mods folder match the server list. We found people who were still crashing/freezing were being allowed to login despite the server logging an error at their connection of a mod mismatch.
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The last of the freezes/crashes were resolved by utilizing the silentlog folder override trick mentioned by the win7 users that had found it was fixing their crashing. I FTP’d into my server files and made the folder in the Saved/Logs section. Our server personally doesn’t run Battleye, but I was seeing calls to it in the server log regardless. I additionally deleted the .dll files in the Binaries folder tree as a precaution.