I'm sorry for the delay, download the game again, the bug has been fixed.
It must be a conditional thing then, cos Amara's Route didn't appear once in the entire time I was going through it - from the very beginning, I couldn't see it, and had to guess when I had to speak to her to progress. The only thing I can think of that might be a factor was that I went straight to Confidence 2 before speaking to her, when the quest requirement was only Confidence 1? I'll do some more testing and see if I can figure out a trigger condition, or if it was a one-off