I know one sure fire fix that will work for you, cause the mod is save game compliant for sure. Uncheck the APP mod and load up your save, it will spit warnings at you cause you removed a mod, just click yes, get in game, save, exit, recheck the mod, load your game. That will let you pull the mod out of the Load, so your game states it is not present, and when you readd it to the save it should kick in like a charm.
I tried this jury-rig, and it didn't work, unless I did it wrong. I disabled APP in FOMM, started the game, loaded up a game that was post-character selection (i.e., after "Escape!"), saved it with the mod unloaded, exited the game, re-enabled APP, and loaded that save. Still doesn't work. Guess I'll just have to wait for the update.