If you haven't played with the mod from the start and chosen all extra stories, you won't be able to see all the scenes so far. The mod only accounts for the total number of things from the start of the game and extras in each update.
Unless I've misunderstood what you mean... I
have played with your mod since it was first available (forget what version that was) and used it each time to see
all available stories. On the next release, I waited until you updated your mod, added it, and did the same as above. Same with this release, though I did load that old save from Allison story 14 and played from there. That could be related somehow, I guess.
But I'll try the console command you mention. Thanks.
EDIT: While using that console command at the end of one story did get me back to the choice menu, at the end of each story it dumped me back into the console rather than the choice menu again.
Repeating the command did seem to advance the stories, but when I got to the "end" of all stories and chose that final menu item (rather than being forced to the screen with Ifuma staring sort of into the camera) I had only two lovers from which to choose the ending, even though all the xxxxxx_lover flags were set for all of them..
At this point I think I'll just hold off dicking with it further and wait for the next release, then pick up at the point where this issue started.