I'm not entirely sure, but I believe the issue is caused by this mod. While playing, npcs, homies or otherwise, have a problem moving on stairs. As soon as they get on the first step, they start moving very slowly, but still using the running animation. It is a problem because they are way behind me on any missions with stairs.
Edit: Sorry to have blamed you, a clean install still has this problem, I just don't recall ever seeing it before.