I have gone through this a few times, searching for answers and trying to come up with a solid interpretation of this mystery for myself. This did not happen to me on my first playthrough: I found that if you press Escape to close a Journal Entry instead of Return, it can prevent you from opening other Entries or using most of the menu options. Going Back a step before this can fix it or by making a Quick Save/Load.
The reading level for this was a little higher than I am comfortable with, but I tried my best to comprehend it as I went along. My favorite parts to read would be whenever Didi walked across a part of the ruins, a good amount of text in a lonely transition. I think this does a great job from the novel side, fueled further in atmosphere with the selection of sounds, music, and discordant backgrounds.
Can’t figure out why exactly, but I felt very drawn in after reaching the tree. Machines in the ruins? Sure. Pool room? Expected. Mattress laid out next to a seemingly harmless tree? Eerie. I can only imagine what it would have been like from Gogo’s perspective with no one else around.
Entry Nine was the only piece I had misunderstood, thinking that the answer was going to be “at least one of each.” A few specific things took me out of it, wondering what a “pregnant pause” means (I have since looked it up), the use of “betray” in both “failed to betray” and “betraying no traces,” and finally, “Wuzzat?” Haha.