It seems there is one cutscene that messes things up. I tried skipping some of them and none broke the sprinting. Concubine cutscene was also skipping properly (First skip put you right before the choice, second skipped the rest. Skipping while selecting the answer was impossible). I will try and search for the broblem towards the end of the week, but if you could remember which cutscene broke sprinting, that would make things much easier for me.
Pause button for cutscenes is something I plan to do in the upcoming days. The whole cutscene skipping system is not great so I will try to improve it too.
You get the citizenship by finishing a simple quest. Talk to Billy about delivering the letter and after that about higher circles. Go to riverstone and go to the mayors house.
Edit.:
The cutscene that might have broken sprinting probably was the one where you meet the german general for the first time. Tell me if you find another one.
Also, I managed to make pausing cutscenes work. Will need more testing to make sure everything works correctly.