Hey! I recently had to change LuckPerms storage method because of this. MySQL server is stable, the server is used by other plugins, and they all work well. My maximum-lifetime was set to 10 minutes, exactly like MySQL wait_timeout (yeah, it should be less, but it shouldn't kick everyone from the server). Server log: hastebin
My previous config: hastebin (confidential data removed)

It's probably not LuckPerms that's timing out the players - I'd guess something else is causing high network latency, or the server is overloaded in some other way.

I don't think there's a LP bug here.

There's some more info you can find here https://github.com/lucko/LuckPerms/wiki/Storage-system-errors that might be helpful. :)