I'm really not sure if I can attribute Hanlon's razor to this. When you log in, that's by definition hitting the database, and should return your settings. Place that in a cookie/localstorage and it should still know your settings offline.
I'm pretty sure I saw in an AMA that Reddit has an Accounts database (maybe split further by sharding) which I'd assume holds your settings as well.
But I rescind my point; it could very well be attributed to database infrastructure issues, whether that's hitting a shard with stale data, or splitting account settings to its own DB that it can't access when you log in.
