everytime i start a new game and go to the vigor machine to get my special points assigned i interact with it and it doesn't pop up the menu like usual.
i do have several mods like the free play after mq enabled and a few starter pack mods and such.
I'm assuming you already tried disabling your mods and then starting a new game with the intent of re-enabling those mods after you finish character creation.
So the next thing to try would be bringing up the command console, targetting the vigor machine and entering the "activate" command.