Could RPU have something to do with addicts stopping in doorways in the Den? Weirdly I don't think I've ever had this happen before, but this playthrough I've been forced to gun down at least two addicts (thankfully, no one around cares). Seems unlikely to be the RPU, but literally nothing else has changed for me.
Edit to add: .Pixote., does the dat you uploaded include script changes for quests? I saw earlier in the thread that you would need someone to do that (specifically in reference to plants at the EPA), but if that got handled for those maps I'm happy to test them, particularly while I'm so early in a playthrough that restarting is trivial.
Edit2: Also, Pix, the NMA links in your sig are all dead for me; looks like the site might have changed formats since you saved them?