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I believe I chose the right pendulum (I can't remember the color off the top of my head) on my first run and was able to open the door. Second run I chose left and teleported. After that I alternated between each pendulum a couple times and from what I can tell I could do either. I would see the teleport glow and then go through the door, for example. I used continue each time, so it probably is related to the inventory persistence bug.

One last thing I just remembered. The two ghosts weren't able to hurt me after the second run (I'm not sure if they could before that since I was too spooked to do anything but mash F and C).

Ok interesting, I'm pretty sure I fixed the inventory persistence bug. The problem was I had used buttons for the icons and set active/inactive images, and apparently those states don't get stored in saves. But the actual value that is checked to see which pendulum the player has was unaffected, it reverted back to 0 (no pendulum) like it should have when the autosave is loaded. So it seems like this is a different issue, I'll see if I can replicate what you are describing tonight and hopefully get it fixed.