It's really difficult to say why you are having these problems after the latest update, since we fixed the issues related to items in the game (door knob, collectibles, etc.) in the 1.1.0 update that was released in early July (you can see the discussions
here and
here). We have had no reports of this issue since the 1.1.0 version was released, until now.
If you skipped that update, or if you started your game over (or it reset on an earlier version), it's possible that you're experiencing the corruption that we fixed in June. If that's the case, probably the only way to clear the problem is to start the game over using the Start Over function on the main menu screen. That has been the only way that we have seen to fix a corrupted game.