So, I also have this problem every time a new Story Girl is released, and I think I know what the problem is. Did you craft "Bunny's Sex Toy" with your Mojo? It gives you a percentile chance of skipping non-boss Stages. I think that might be screwing with how girls are being detected and acquired, like possibly the girls are awarded on Stage 501, instead of 500, and after the Boss the game just "skips" 501 so you lose credit. Ever since Trascending started reseting your Crafts, I stopped unlocking Bunny's Sex Toy, Dirty Talking Script (having more time on the Boss doesn't really guarantee you'll win, better off losing and claiming money from normal Stages, especially if your AFK grinding) and Mojo Runic Wallpaper (it causes the game to freeze after Resets, due to the sudden burst of damage)
Although, more than likely, your damage is just so high that the game isn't able to register your progress to give you the girl. Usually after a dozen or so Resets, I eventually get the girl. You have to reset anyway, to increase your Maximum Stage limit, so your bound to unlock the girls, sooner or later.