Good news! I did a systematic sweep of the whole house checking every blue item spot (finding several missed hint coins in the process, hooray!) and finally located the rock! It had respawned in one of the safes, possibly the safe where I had originally gotten it from, which I am fairly sure is not where I left it (as I said, I had put it in front of a gargoyle to try to solve that puzzle). It seems a little hinky whether certain items spawn in the chest or not? The scissors have been showing up in there pretty reliably, but the kitchen puzzle pieces ALL showed up in the chest one time and then never again on any subsequent login, staying on the table where I left them. Anyway, I located the rock and also some paper at long last, so that puzzle is finally checked off!