Yes, thank you to Gi Nattak for finding the bug and finding a fix for it before I even got a chance to look at it!
It only happens if you recruit Cyan BEFORE you recruit Leo. The code that skips the line telling you where to find Cyan jumps 1 byte too far, putting you in the middle of a function. I'll work at getting patch 1.31 together over the weekend, but if you have a hex editor, you can fix this right away.
1. Open your Divergent Paths rom in your hex editor.
2. Go to address 0Cx4273 in an unheadered rom, or 0Cx4473 in a headered rom.
3. Change the value from 7B to 7A and save.