I apologize but it is my policy to only spend time on bugs that come up in the base game, rather than a modded game, as I cannot control what code mods add and it turns the game code into an unknown quantity for me... have had a few bad experiences of spending hours looking for stuff that turns out was mod conflict related.I saved right before going to the new-U station and repeated that part 3 times. It's never once said anywhere I got a side effect and every time I get stuck. So if it did have a side effect then it's happened 3 times in a row without providing notice that it happened.
While it shouldn't be important, this is a modded game, but the mods are just the body pillow mod, DatDude's Demo Experiments, the BR Pill Mod, and the drug framework. None of which should be changing anything here...
If possible if you could reproduce this in the core game and send me a save file of the day before the pill wearing off (by turning on autosave), then I could work out what is going on if it is still happening in the base game.