I'm also having this problem. I've completed Master Diver twice and I go down the list, 1 key per day. I got stuck on the third round, 6 out of 10 done. All the chests appear open now, even ones I haven't opened according to my checklist. I collected 1 key and checked the sunken chests each day since but no luck. Now have 4 keys. But before that, I'd only have 1 key in my inventory at a time so I don't think that's what broke it.