I finally got around the problem by starting anew (deleting appdata saves, unpacking the game into a new folder, if that matters) and after opening the portal room I didn't use gems to light it up immediately as I done before but waited until I paid off the debt, and the button was where it should be this time.
If I may offer a preventive solution for potential reoccurrence of this issue, you should make portal activation action (putting gems in) available only when you get rid of the debt and are ready to receive Nyx. There are lines about you receiving instructions about portal operation from the guild at that point, so it only makes sense, and saves you the scrolls you'd waste otherwise.
I have other suggestions, if you'd like them:
Give a more obvious hint in-game that there's some reward for bringing a large sum up in one go (I discovered the reward accidentally, but some might miss it if they give her less than 5001 gold all the way, or save up until they have full sum ready, because IIRC you don't get a reward for the last haul, even if you bring her hundred grand at once). When she sends you down initially, and when she throws you out of her room in the morning would be a good place for a reminder.
Extending the 18:00 events to 19:00 or ending the portal minigame & Nyx looting at 18:00 might also be a good idea.
Other than that, gotta say you've done a pretty stellar job. The models are great, the game's pretty well put together, I've yet to figure out how to bring Nyx to brothel but other than that portal problem I didn't need the guide at all (but it's good that you made it). Oh, and portal game is a slog, and after you take all free squares seeing the numbers rise behind the barrier is a bit disheartening. I've done it once, but I really hope you'd make a "start from act 3" with it fully conquered.