1/3
3 Years of Service
Could you give some examples, because I just skipped through the game thrice and didn't notice any missing choices (once with my old saves intact, once more with fresh saves, and again after that with fresh saves and dev mode/console disabled in case that was doing something).I'm gonna say this:
I used the main download on the front page and choices WERE in fact missing. However, this is due to the "Define" flag for most variables being placed AFTER the choice menu, making it so certain choices just don't show up. If you manually go into the rpy file and cut those variables and paste them before the choices, all available choices show up.
The placement of defaults/defines doesn't really matter; if it did, the game would throw an error the first time you talk to Hiroko at the orphanage.